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Staphylococcus aureus metabolic requirements during skin colonization

Project Summary Staphylococcus aureus causes 76% of all skin infections, and yet simultaneously this pathogen asymptomatically colonizes the skin of 8-22% of healthy adults. Since the majority of S. aureus disease is the result of autoinfection from the colonizing strain, and invasive infections often originate from the skin, there is an urgent need to understand colonization mechanisms. In colonizing the skin, S. aureus encounters abundant levels of amino acid derivatives like urocanic acid and 5-oxoproline (OP) that contribute to the skin’s “acid mantle” and have reported anti-Staphylococcal properties. The central hypothesis of this project is that amino acid transport and catabolism is a critical feature of S. aureus skin colonization. To model this environment, we developed a skin-like media (SLM) to assess S. aureus physiology on the human skin surface. We determined the S. aureus transcriptional response using RNAseq and performed metabolomics in SLM, both of which demonstrated that amino acid catabolism genes are upregulated and that amino acids are rapidly consumed. These findings indicate that S. aureus has a skin expression program that enables survival and growth in this harsh environment. In Specific Aim 1, we are investigating S. aureus metabolism of serine, the second most abundant amino acid on human skin. We hypothesize that serine transport and catabolism is critical for S. aureus skin colonization. We will assess growth of mutant strains disrupted in serine pathways in the SLM and during mouse skin colonization. With 13C-tracing experiments we will investigate serine flux in S. aureus using metabolomics. We will determine serine transport mechanisms using bioinformatic guided targets and serine analogues. In Specific Aim 2, we will assess S. aureus resistance to toxic skin metabolites. OP is abundant on human skin and is known to be deleterious to bacteria. Our preliminary metabolomics studies indicate that S. aureus metabolizes OP in SLM, and we have identified a putative oxoprolinase (genes SAUSA300_1566-1561) that is upregulated on skin. We hypothesize that the detoxification of OP contributes to S. aureus survival on the skin. We will construct mutants in the 1566-1561 locus and test their contributions to OP metabolism in SLM with growth and metabolomics experiments. We will also investigate OP transport and test mutant strains in our mouse skin colonization model. In Specific Aim 3, we will identify new determinants of S. aureus skin colonization using TnSeq. We have developed an improved TnSeq library preparation and analysis protocol, and in our preliminary studies we performed TnSeq in SLM and in our mouse skin colonization model. We will evaluate pathway hits, such as respiration and fermentation, and aspartate metabolism targets by testing constructed mutants during SLM growth and in the mouse model. Novel hits will be validated with follow-up genetic experiments and 13C-tracing experiments. Collectively, the proposed studies will advance our knowledge of S. aureus colonization and adaptation to the skin environment.

Short-wave infrared Cerenkov imaging to better visualize targeted radiotherapy and diagnostic radiotracers

SUMMARY. The problem: Cerenkov luminescence (CL) imaging (CLI) is a new imaging method that utilizes light emitted during decay of radiotracers. CLI merges optical and nuclear imaging by utilizing affordable yet highly sensitive optical cameras with clinical radiotracers. It provides fast and cheap clinical optical imaging to explore radiotracer distribution in patients. While not tomographic, CLI systems have a lower price, smaller footprint and higher resolution than nuclear imaging scanners. Yet, due to the very low signal intensity of CL its versatility remains limited since CLI requires strict exclusion of ambient light with an enclosure. Therefore, CLI requires novel approaches to make clinical imaging more feasible. We hypothesized that we could explore the short-wave infrared (SWIR) part of CL to enable CLI under ambient light without enclosure, providing improved and facile CLI, particularly of isotopes used for therapy that cannot be imaged otherwise. SWIR imaging (900- 1300 nm) has almost no autofluorescence, absorption or scatter but provides significantly higher depth penetration, yielding images with higher contrast and resolution compared to the visible range. Since typical LEDs do not emit light beyond 850 nm, they do not interfere with the SWIR camera. We can therefore perform CLI in the SWIR range (SWIR-CLI) without the limiting light-tight box and under ambient LED light and also achieve better signal penetration and accuracy. We will investigate if SWIR-CLI can be used to monitor distribution of therapeutic isotopes for targeted radiotherapy (TRT), a fast-expanding field as highlighted by Novartis’ acquisition of Lutathera and Pluvicto for the price of $6 bn. These agents are targeting 177Lu as therapy to neuroendocrine and prostate cancers. For TRT α-emitting isotopes are particularly attractive due to the α- particle’s short path length with high linear energy transfer. However, α-emitters are very difficult to image with conventional equipment. The α-emitter could be swapped with an imaging isotope, but this can alter the agent’s biodistribution. The α-particle itself does not have sufficient energy to produce CL but several daughters in the decay chains of most α-emitters produce electrons with sufficient energy to create CL. We have already imaged the α-emitter 223Ra in patients and have recently shown that CLI of α-emitters in the SWIR is possible. SWIR- CLI could therefore provide a facile imaging approach for α-emitters. We will answer with our three independent Aims the following questions: (1) Can we image diagnostic isotopes with SWIR-CLI? (2) Can we image therapeutic emitters with SWIR-CLI? (3) Can we use SWIR-CLI to image patients undergoing PET and/or TRT? Animal studies will employ established mouse cancer models to optimize imaging parameters and validate findings, directly informing the co-clinical Aim 3 trial. By eliminating the requirement for a light-tight enclosure and enabling CLI under ambient light, SWIR-CLI represents a significant shift in the practical deployment of CLI rather than an incremental improvement. Our study will broaden the reach of CLI by enabling imaging under ambient lighting, unlocking innovative new opportunities for CLI (monitoring TRT) in research & clinical settings.

Weak Cell Adhesion is a Prognostic Signature of Invasive Cancer

Project Summary Despite early detection, low-grade and localized breast cancers such as ductal carcinoma in situ (DCIS) can relapse in up to 20% of cases despite standard of care. For DCIS, relapse affects over 12,000 U.S. women annually and has increased 60% in the last 40 years. Current diagnostic assessments including histopathological markers often miss early disseminating cells, lack specificity, or cannot distinguish cancer from non-cancer cells in the stroma. Hence there is an unmet need for cancer diagnostic technologies that employ radically different characterization methods. For example, significant physical differences exist between metastasizing and benign breast cancer cells, owing to metastasizing cells detaching from the primary tumor, migrating through the surrounding stroma, intravasating and extravasating, and ultimately engrafting in distant tissues. We recently demonstrated that cancer cells with weaker adhesion migrate faster and metastasize more frequently in murine breast cancer models than strongly adherent cells. In a small pilot study of human breast tumors, we also observed that the abundance of weakly adherent (WA) cells scales with disease severity; subpopulations from invasive carcinomas were the least adherent. However, a subset of DCIS cases displayed much less adhesion, suggesting that these patients may have a tumor subpopulation that progresses to metastatic disease despite standard-of-care treatment. Weak adhesion is a defining physical characteristic of tumors, but to establish their role in initiation, metastasis, and patient outcomes, we will leverage model systems and our newly patented adhesion technology to answer these fundamental questions of cancer biology and clinical translation. To understand the impact of adhesion on cancer progression, we will evaluate the tumor-initiating potential of WA versus strongly adherent (SA) tumor cells in a murine breast cancer model before confirming how weak adhesion advantages cells to cause secondary disease using bioengineered in vitro models. In dissecting the stages of metastasis where WA cells exhibit advantages, e.g., recapitulating stromal niche, transendothelial migration, and tissue-specific colonization, we will identify mechanisms that enable WA cells to thrive and evaluate therapeutic targets that disrupt these pathways. Finally, we will analyze the adhesion profiles of resected tumors and stroma from 80 breast cancer patients with DCIS or invasive disease. Adhesion data will be correlated with conventional assessment methods and ultimately with patient outcomes, e.g., disease-free and progression-free intervals. We anticipate that the DCIS subpopulation that aligns with the adhesion signature of invasive carcinomas will have shorter intervals and survival time. This integrated study design bridges mouse models, mechanistic bioengineering assays, and human samples to clarify the metastatic potential and prognostic value of WA breast cancer cells. Our use of mouse models in this grant is required to study the interactions among tumor cells, immune cells, vasculature, and stromal tissues that drive tumor formation in vivo. Bioengineered in vitro systems lack the complexity to ask such questions and using injected tumor cells is not possible in humans.

Defining Microbial and Host Pathways Driving Asymptomatic C. difficile Colonization Associated with Aging and High-Sugar Diets

SUMMARY Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhea, with rising incidence in community settings and a growing burden of asymptomatic colonization. Asymptomatic car- riers, particularly among the elderly and individuals consuming high-sugar diets, represent a critical but underexplored reservoir for transmission and disease progression. This proposal introduces novel, anti- biotic-independent mouse models demonstrating that both dietary sugar and aging independently pro- mote asymptomatic C. difficile colonization. We hypothesize that these factors disrupt colonization re- sistance (CR) through distinct but overlapping microbial, metabolic, and immune pathways. In Aim 1, we will define how traditional and emerging dietary sugars alter the gut environment to permit C. difficile colonization using in vitro bioreactors and in vivo models. Aim 2 will identify age-associated changes in microbiota and mucosal immunity that impair CR, using longitudinal studies and fecal micro- biota transfer. Aim 3 will functionally validate C. difficile genes upregulated during asymptomatic carriage using CRISPR-Cas9 mutants in both sugar- and age-induced models. This integrative, multi-omics approach will uncover the mechanisms enabling asymptomatic colonization and identify microbial and host targets for intervention. The findings will inform microbiome-based strat- egies to prevent CDI in vulnerable populations and shift current paradigms in CDI risk assessment and prevention.

The Role of the Intestinal Microbiota in Sepsis Mortality

Project Summary/Abstract Sepsis is a life-threatening condition characterized by a dysregulated host response to infection that can cause multi-organ damage and death. As the leading cause of in-hospital mortality, sepsis mortality rates reach up to 50%, and account for approximately 270,000 deaths and $38 billion annually in health care costs in the United States. Notably, patients with similar medical backgrounds can have vastly different sepsis outcomes— some survive with medical treatment while others die. The reasons for this dichotomy are unknown but is seen across all forms of bacterial bloodstream infections, is not specific to any strain-level differences in the infecting pathogen and cannot be explained by human genetic differences. Human microbiota studies suggest that gut microbial dysbiosis is associated with sepsis mortality and that these alterations influence gut barrier breakdown, leading to gram-negative bacteremia—one of the most common causes of sepsis and mortality. However, there are a lack of studies that investigate the causal role of the intestinal microbiota in sepsis mortality. This K08 proposal will elucidate the role of the intestinal microbiota in sepsis mortality. Utilizing the well- established murine model of sepsis by intraperitoneal injection of lipopolysaccharide (LPS), we combine microbiota taxonomic sequencing and metagenomics, advanced bioinformatic techniques and prediction modeling, with knowledge of mucosal immunity and germ-free mouse systems to characterize the microbiota features and members that correlate with, predict, and cause sepsis mortality. This proposal is organized into two specific aims: (1) identify baseline stool microbial features associated with and predictive of sepsis outcomes and (2) determine how colonization with immunostimulatory microbes heightens sepsis mortality. In this work, I will holistically characterize the host immunologic and microbiota features that are associated with and predictive of mortality and experimentally identify microbes and microbial pathways that cause death in our model. These findings will reveal new microbial and host biomarkers of sepsis mortality and identify novel targets for sepsis prevention and treatment to reduce the overall mortality rate of this deadly disease. My long-term goal is to become an independent physician-scientist who integrates cutting-edge computational methods with experimental biology to identify predictive biomarkers of disease onset and outcomes, investigate how they influence disease processes, and develop novel therapeutic and preventive strategies to improve patient care. This proposal details specific research aims and a structured career development and training plan that will allow me to acquire focused, in-depth and multidisciplinary training under the guidance of an internationally recognized team of experts in clinical infectious diseases, host-microbiota interactions, immunology, immunometabolism, and computational biology. The knowledge generated will address the fundamental role of the microbiota in sepsis outcomes and inform future preventative and therapeutic strategies that will lower the sepsis mortality rate worldwide.

Causal mechanisms driving germline predisposition to myeloproliferative disorders

SUMMARY/ABSTRACT Although human genetic studies have indicated a significant hereditary predisposition to myeloproliferative neoplasms (MPNs) the underlying mechanisms driving the genetic risk remains unknown. Our large genome wide association study (GWAS) on MPNs identified several non-coding genetic risk loci associated with disease and implicated modulation of hematopoietic stem cell (HSC) self-renewal by the genetic variants. The long-term goal is to utilize our GWAS results to better understand MPN disease initiation and progression and draw out key unknown MPN predisposition genes. The overall objectives in this application are to elucidate the mechanisms by which MPN risk variants promote disease initiation and progression. The central hypothesis is that common genetic variants increase MPN risk by affecting regulatory elements that influence clonal expansion of HSCs carrying MPN driver mutations. The rationale for this project is that the HSC clones with most prevalent driver mutation found in MPN, JAK2V617F show individual specific growth rates and can develop into MPN or remain as clonal hematopoiesis without any consequences indicating that germline genetic factors influence this process. The central hypothesis will be tested by pursuing two specific aims: 1) To determine the mechanisms by which genetic variation at the GFI1B locus influences MPN predisposition in vivo. 2) To define upstream transcriptional mechanisms disrupted by common genetic variants that predispose to MPN. Under the first aim, a newly generated mouse model will be used to evaluate clonal expansion of JAK2V617F HSCs in the context of a germline Gfi1b enhancer deletion by in vivo competitive transplantation assays. The murine studies will be complemented by an assessment of Gfi1b allele specific clonal expansion in primary human hematopoietic stem and progenitor cells (HSPCs) engineered to carry JAK2V617F mutation. Mechanistically activated mitochondrial respiration will be examined in germline enhancer inactivated JAK2V617F HSPCs in murine models and human patient samples. For the second aim, perturbation of RUNX1 bound cis-regulatory elements by MPN risk variants will be evaluated as a mechanism of clonal expansion in MPN by using lentiviral reporter assays and endogenous CRISPR/Cas9 editing approaches in primary human HSPCs and degron tagged RUNX1 cell lines. A Runx1 haploinsufficiency mouse model will be used to assess global influences of RUNX1 transcriptional network on MPN initiation. Collectively, our proposed studies aim to bridge the gap between inherited genetic variations and the clonal expansion dynamics of MPN stem cells, shedding light on crucial factors influencing disease development. The mouse models proposed in this study provide the in vivo physiological context and functional readouts required to investigate HSC clonal expansion and MPN pathogenesis.

Targeting VIP–VPAC Signaling to Reverse Immune Exclusion and Enhance Immunotherapy Response in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer that is largely unresponsive to chemotherapy and current immune checkpoint blockade drugs, highlighting a critical need for the development of innovative therapeutic strategies. This R01 proposal targets vasoactive intestinal peptide (VIP), an immunosuppressive neuropeptide overexpressed in PDAC, which signals through VIP receptors (VPAC) on cancer cells, T cells, and myeloid cells within the tumor microenvironment. Based on our recent success in developing selective and potent VPAC receptor antagonists, we hypothesize that blocking VPAC signaling will reverse immunosuppression in the PDAC TME by reducing immune checkpoint expression, enhancing chemokine-driven infiltration of cytotoxic T cells, and disrupting immunosuppressive interactions between T cells and myeloid cells, ultimately leading to durable anti-cancer immunity. We propose three specific aims to explore the immunosuppressive roles of VPAC signaling in PDAC. Aim 1 will identify the primary sources of VIP in PDAC tumors and characterize the effects of VPAC signaling on immune cell function and phenotype within the tumor microenvironment. Aim 2 will investigate how VPAC signaling influences immune cell migration into tumors by modulating chemokine receptors and directional signaling. Aim 3 will determine how VPAC signaling regulates interactions between T cells and immunosuppressive myeloid cells, particularly tumor-associated macrophages, and the resulting impact on anti-cancer immune responses and immunological memory. Our preliminary findings indicate that combined inhibition of VPAC signaling and PD-1 significantly enhances the regression of PDAC tumors in multiple mouse models, generating lasting protective immunity in cured mice without triggering autoimmune responses. We will use novel methods to pursue our aims, including inducible genetically engineered mouse models (GEMM) of PDAC, long-acting VPAC antagonists engineered with immunoglobulin Fc domains to improve their plasma half-life, and advanced microfluidics technologies to analyze immune cell movement within tumors. Animal experiments will be used to validate the translational potential of observations from in vitro organoids and microfluidic experiments. The GEMM and orthotopic mouse models of PDAC are necessary to provide critical insights into the 3-D structure of the TME and tumor regression in response to our novel immunotherapy. This research will be conducted by a multidisciplinary team with complementary expertise that will clarify the therapeutic potential of VPAC signaling inhibition in PDAC using sophisticated experimental tools and single-cell RNA sequencing. Ultimately, these findings could significantly improve the development of immunotherapeutic strategies for PDAC, potentially enhancing patient outcomes in pancreatic cancer and other malignancies expressing high VIP levels.

Exploring in vivo Treg function in T1D through the lens of expanded Tregs

PROJECT SUMMARY/ABSTRACT A critical barrier to optimally treating Type 1 Diabetes (T1D), an autoimmune disease in which the islet beta cells are destroyed by immune cells, is understanding how autoimmunity is regulated in vivo. Several lines of evidence suggest that defective CD4+FOXP3+ regulatory T cells (Treg) likely contribute to the loss of tolerance in T1D. Yet, less is known about how human Treg function in vivo. In the Sanford T-rex study in which adolescents diagnosed with T1D were treated with a single dose of polyclonal autologous in vitro expanded Treg (expTreg), we found that a lower degree of in vitro Treg expansion significantly correlated with better preservation of C- peptide (a biomarker of insulin secretion and beta cell function) a year after treatment. This correlation could not be explained by age, expTreg phenotype or in vitro expTreg suppressive function. However, we did identify an expTreg gene signature that correlated with better C-peptide preservation and this expTreg signature was consistently expressed over time within individuals. Further, lower- and higher- expTreg differed phenotypically and transcriptionally by signatures implicating metabolic, homing and suppressive functions. Together, these data suggest that intrinsic features of an individual’s Treg may contribute to the extent of in vitro Treg expansion. They also suggest that strong activation and expansion can differentially amplify or alter the state of Tregs, leading to changes in homing and function that may impact clinical response. Based on these findings, we hypothesize that Treg proliferative capacity is driven by the activation and metabolic state of Treg resulting in differential in vitro fold expansion, homing potential and in vivo suppressive function that impacts clinical outcome. We will test this hypothesis by leveraging existing primary human samples from both the T-rex clinical trial and the Benaroya Research Institute Registry and Repository that includes individuals with known degree of in vitro Treg expansion and known C-peptide decline. In Aim1, we will identify how activation states of pre- and post- expansion Treg and longitudinal Treg in T-rex participants contribute to proliferative capacity and outcome using cellular, transcriptomic and epigenetic assays. In Aim 2 we will determine how metabolic shifts during Treg in vitro fold expansion alter Treg suppressive function, thereby impacting clinical outcome. In Aim 3, we will compare the in vivo suppressive function of lower- versus higher-expTreg from clinical samples using a xenogeneic graft versus host disease (GvHD) mouse model in addition to assessing in vivo expTreg homing and function using the assays from Aims 1 and 2 and a novel in vitro assay of cell trafficking to pancreatic islets. Successful completion of these aims will reveal mechanisms regulating Treg proliferative capacity and in vivo function that impact clinical outcome. Understanding these mechanisms will guide development of next generation Treg activation and expansion protocols for Treg therapies and help tailor the Treg expansion process to an individual’s baseline Treg signature.

Structural and functional characterization of autoimmune antibodies against NMDAR

Project Summary. The goal of this project is to understand the origins and molecular mechanisms underlying the anti-cancer autoimmune response against the N-methyl-D-aspartate receptor (NMDAR) and its correlation with anti-N-methyl-D-aspartate receptor autoimmune encephalitis (NMDARAE). While anti-cancer immune responses can promote tumor elimination, they may also lead to the production of self-reactive antibodies that trigger autoimmune diseases. NMDARAE is the most common form of immune-mediated encephalitis, which results in prominent neuropsychiatric symptoms, including seizures, psychosis, and memory deficits. NMDARs belong to a family of ligand-gated ion channels expressed exclusively in the central nervous system. They are involved in various aspects of brain development and function, including learning and memory. They respond to the neurotransmitter glutamate and a co-agonist, glycine or D-serine, to mediate excitatory neurotransmission, which plays a central role in synaptic plasticity. NMDARAE is associated with ovarian teratomas, where aberrant NMDAR expression is believed to trigger an autoimmune response. In NMDARAE, anti-NMDAR antibodies, as well as B cells and antibody-secreting cells, cross the blood-brain barrier via unknown mechanisms, resulting in the presence of anti-NMDAR antibodies at high titers within the brain and cerebrospinal fluid (CSF). These antibodies target NMDARs, modulating their function and contributing to disease pathology. Emerging evidence, supported by our preliminary data, suggests that NMDARs are also expressed in triple-negative breast cancer (TNBC), extending the relevance of anti-NMDAR autoimmunity beyond ovarian teratomas. In our TNBC mouse model, which ectopically expresses NMDARs (TNBC-NMDAR), we observed the onset of anti-NMDAR autoimmunity, where the produced antibodies cause both anti-tumor activity and symptoms such as lowered seizure threshold, mirroring key features of NMDARAE. Here, we will establish this TNBC mouse model as we develop molecular methods to characterize it. Aim 1 will focus on establishing and characterizing the TNBC- NMDAR mouse model. We will develop a detection method utilizing the intact tetrameric NMDAR channel proteins and a method to isolate B cells expressing B cell receptors against NMDAR from biological samples by using fluorescently labeled intact NMDAR proteins, followed by single-cell RNA sequencing. Aim 2 will utilize single-particle cryo-electron microscopy (cryo-EM) to investigate the interactions between NMDAR and the cloned antibodies, providing insights into epitope recognition, NMDAR subtype specificity, and conformational changes induced by antibody binding. Aim 3 will assess the impact of the cloned antibodies on NMDAR channel activity using electrophysiology. We will also assess anti-tumor activity and NMDARAE onset by each antibody clone. Together, the proposed research will gain insights into the link between anti-cancer anti-NMDAR autoimmunity and NMDARAE. It will also elucidate which functional properties of the cloned antibodies promote anti-tumor activity while contributing to NMDARAE, thereby informing potential therapeutic strategies.

Utilizing integrin-targeted PET imaging and therapeutics to predict and treat radiation-induced pulmonary fibrosis

Project Summary/Abstract. Lung cancer is the leading cause of cancer death in the US, with over 125,000 deaths annually. Radiation therapy (RT) is a critical component of curative lung cancer treatment for many patients. However, radiationinduced pulmonary fibrosis (RIPF) is a common side effect that carries a poor prognosis with limited treatment options. Up to 40% of patients with lung cancer who receive RT may experience RIPF. RIPF is a late effect of RT, typically occurring 3 or more months after treatment. The symptoms of RIPF can include shortness of breath, pleural effusions, decreased lung function, and respiratory failure. Cell surface integrin heterodimers play a key role in the pathogenesis of RIPF. In particular, the integrin αvβ6, which is expressed at a low level in the alveolar epithelium at baseline, is significantly upregulated upon RT damage. The key role of integrin αvβ6 in RIPF is illustrated by studies in which mice lacking integrin αvβ6, or treated with an αvβ6-blocking antibody, do not develop RIPF. Here, we propose to translate this mechanistic understanding of RIPF into novel approaches for monitoring and treating RIPF. We hypothesize that non-invasive αvβ6 PET imaging will be safe and can specifically bind to αvβ6 in patients with RIPF. Additionally, we hypothesize that a novel small-molecule integrin antagonist, IDL2965, can mitigate and treat RIPF in mice. In this project, we are utilizing mice to model RIPF, as mice develop RIPF that mimics human disease. In addition, cellular and in vitro models do not approximate the complex biology leading to the development of RIPF. Our data using [64Cu]Cu-DOTA-αvβ6-BP to detect early RIPF in mice are compelling in both single-fraction high-dose RT and lower dose-larger volume RT models (Lo et. al, IJROBP 2025). However, to progress to clinical trials in patients with cancer, we will obtain data to submit an Investigational New Drug (IND) application to the FDA. Importantly, we propose translating [64Cu]Cu-DOTA-αvβ6-BP PET imaging into patients with lung cancer, allowing us to better identify RIPF and develop a tool to determine the efficacy of IDL-2965 in future clinical studies. The specific aims of the proposal are: (1) Characterize the utility of [64Cu]Cu-DOTA-αvβ6-BP in mice with conventionally fractionated RT and identify circulating biomarkers of RIPF, and determine the in vivo toxicology of [64Cu]Cu-DOTA-αvβ6-BP to prepare and submit an exploratory Investigational New Drug (eIND) application to the FDA, (2) Conduct a first-in-human clinical trial of [64Cu]Cu-DOTA-αvβ6-BP to determine its safety and human dosimetry in patients with evidence of RIPF from computed tomography or in healthy controls, and (3) Determine the effect of integrin antagonism using IDL-2965 on mitigating RIPF in preclinical mouse models. The goals of this proposal are two-fold: (1) demonstrate safety and target specificity for [64Cu]Cu-DOTA-αvβ6-BP so that it can be used in future studies to identify RIPF and evaluate the efficacy of anti-fibrotic therapies, and 2) determine the ability of IDL-2965 to prevent RIPF in preclinical mouse models.

Delineating the role of TREM2 in chronic pancreatitis

PROJECT SUMMARY Chronic pancreatitis (CP) is a progressive digestive disorder characterized by persistent inflammation, irreversible fibrosis, and acinar cell damage. However, current treatment options remain limited, underscoring the need for effective, targeted therapeutic strategies through a deeper understanding of the disease microenvironment. Macrophages are pivotal players in the CP microenvironment, exhibiting dual roles in inflammation and tissue remodeling. A defining feature of macrophages is their remarkable phenotypic plasticity, enabling them to transition between pro-inflammatory and anti-inflammatory phenotypes. However, the specific macrophage phenotypes contributing to the immune imbalance in CP and their precise mechanisms of action remain poorly understood. TREM2 (Triggering Receptor Expressed on Myeloid cells 2), a transmembrane receptor of the immunoglobulin superfamily, has emerged as a critical modulator of tissue damage responses in multiple disease settings, though its function in CP remains unexplored. Our preliminary single-cell RNA-seq analyses of human CP tissues reveal an enrichment of inflammatory macrophages alongside a marked downregulation of TREM2 compared to non-diseased controls. This reduction in TREM2 correlates with marked increases in pro-inflammatory mediators, such as IL-1β and NF-κB, suggesting that TREM2 in macrophages contributes to maintaining homeostasis and restraining inflammatory signaling. Accordingly, diminished TREM2 expression appears to skew macrophages toward a pathologically hyper-inflammatory state. We hypothesize that loss of TREM2 disrupts the delicate balance among immune cells, fibroblasts, and acinar cells, fueling a self-reinforcing cycle of inflammation and fibrosis that exacerbates pancreatitis. To test this hypothesis, our R01 will leverage integrative single-cell transcriptomics, spatially resolved imaging, transgenic mouse models, functional organoid co-culture assays, and in vivo experiments to elucidate TREM2’s regulatory mechanisms in CP. This research aims to address two key scientific questions: (1) How does TREM2 suppress pro-inflammatory macrophage phenotypes and restrain IL-1β-induced inflammatory signaling? (2) How does the crosstalk among pro-inflammatory macrophages, fibroblasts, and acinar cells exacerbate the local inflammatory environment, leading to further pancreatic damage? Through this study, we aim to establish TREM2 as a pivotal inhibitory checkpoint in the NF-κB/NLRP3/IL-1β axis, preventing unchecked macrophage-driven inflammation, fibroblast activation, and further acinar cell damage. Successful completion of this project will deepen our mechanistic understanding of CP and identify new therapeutic strategies to mitigate fibrotic progression and preserve pancreatic function. Ultimately, these insights may guide the development of immunomodulatory treatments to attenuate CP severity, thereby transforming the clinical management of this devastating disorder.

Optimization of a novel and effective antiviral agent targeting Zika NS4B

This project focuses on developing novel anti-Zika virus (ZIKV) compounds targeting the NS4B protein, which is crucial for viral replication. ZIKV poses a significant medical challenge due to its potential for severe pathogenic outcomes, such as congenital Zika syndrome and Guillain-Barré Syndrome. Furthermore, its pandemic potential has been increasing with the expansion of carrier mosquito habitats. The project aims to address the urgent need for anti-ZIKV therapeutics that could greatly reduce severity of symptoms and minimize vertical and community transmissions. We have identified a novel small-molecule series with a benzamide scaffold through a cell-based, antiviral ultra-high-throughput screen. This series demonstrates strong potency against ZIKV without measurable cytotoxicity or non-specific antiviral effects, justifying this scaffold as a lead series for further development. Preliminary mechanism-of-action studies, utilizing genetic, biochemical, and virological assays, suggest that this series may inhibit the formation of the ZIKV viral replicase complex by interfering with NS4B. Our goal for this project is to develop a preclinical therapeutic candidate for ZIKV that demonstrates promising therapeutic activity following oral administration in ZIKV-infected mice, at a dosage that shows no clinical toxicity. The project has the following significant and novel objectives: 1) Optimize the benzamide lead for potency and drug-likeness; 2) Develop a lead candidate and a backup compound with optimized pharmacokinetic, pharmacodynamic, and toxicity profiles; 3) Determine the molecular mechanisms of action of the benzamide series using novel structural approaches to assist medicinal chemistry studies; 4) Evaluate the in vivo therapeutic efficacy and safety in mouse models and develop the best therapeutic regime. This project seeks to develop effective antivirals for ZIKV with high retention in the blood and central nervous system (CNS) and high oral bioavailability. The expected successful outcomes will provide significant advancements in ZIKV therapeutics and open new avenues for treating other flavivirus infections

Optimizing CD45-Targeted Astatine-211-Radioimmunotherapy for Malignant and Non-Malignant Blood Disorders

ABSTRACT CD45 is expressed on almost all normal and neoplastic hematopoietic cells but not on non-blood cells and has, therefore, been pursued as a drug target. Initially centered on augmenting conditioning before hematopoietic cell transplantation (HCT) for blood cancers, there is increasing interest in expanding CD45-directed therapies into other settings, with radioimmunotherapy (RIT) being the major therapeutic modality so far. Investigators at our institution pioneered CD45 RIT with b-emitters such as iodine-131 (131I) using the murine monoclonal antibody (mAb), BC8. A phase 3 trial testing 131I-BC8 (131I-apamistamab [Iomab-B]) with allogeneic HCT in older adults with relapsed/refractory acute myeloid leukemia showed improved outcomes over conventional care, validating this approach. More recently, attention has shifted toward a-emitters that deliver substantially higher decay energies over much shorter distances than b-emitters, rendering them more suitable for precise and potent target cell killing. In our work, we focus on astatine-211 (211At) for its ideal half-life and decay without a-emitting daughters. For clinical application, mAbs are conjugated with the bifunctional boron cage molecule, isothiocyantophenethyl-ureido-closo-decaborate(2-) (B10-NCS), to enable stable protein astatination. Three early-phase trials testing 211At-BC8-B10 as augmentation of HCT conditioning for patients with malignant and non-malignant blood disorders are ongoing, with emerging data indicating significant anti-tumor efficacy. Nonetheless, relapses still occur. Other important limitations include marked infusion toxicities and human antimouse antibody (HAMA) responses related to the murine nature of BC8 and dimer formation after 211At labeling of mAb-B10 conjugates with tissue residualization from 211At atom oxidation. The latter may contribute to the risk of liver cell injury, the dose limiting extramedullary toxicity of CD45 RIT. As a first step toward our goal of optimizing CD45 RIT, we have raised new, fully human CD45 mAbs as basis for novel therapeutics. In preliminary in vivo studies in immunodeficient mice, we found some of these mAbs to have greater anti-tumor efficacy than a humanized version of BC8 (HuBC8) we generated as a reference mAb. We will now conduct comparative in vivo CD45+ cell targeting (“biodistribution”) and anti-tumor efficacy studies to select a lead candidate mAb for clinical application and use protein engineering to maximize the selectivity and efficacy of targeted radiation delivery. We will use immunodeficient mice xenotransplanted with human leukemia cells for this purpose as no human approaches are available and in vitro testing is inadequate to measure both the targeting and biologic RIT effects on human leukemia cells. Mice provide the in vivo milieu needed for comprehensive evaluation. Development of improved mAb astatination methodologies to minimize off-target toxicities of 211At-RIT will further increase therapy specificity and reduce toxicity. In parallel, we will conduct genome-scale, unbiased target identification/validation studies to identify partner drugs for rational combination therapies aimed at enhancing the anti-tumor efficacy of 211At-CD45 RIT.

TARGETING VAV1 SCAFFOLDING AND ENZYMATIC FUNCTIONS IN MULTIPLE SCLEROSIS VIA BRAIN-PENETRANT MOLECULAR GLUE DEGRADERS

Abstract Multiple Sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) with significant unmet medical needs, as current therapies offer limited efficacy against neurodegeneration and can have considerable side effects. VAV1, a key signaling protein predominantly expressed in hematopoietic cells, plays a crucial role in T and B lymphocyte activation and is genetically and functionally validated as a therapeutic target in MS. This project proposes an innovative approach to target VAV1 through the development of brain-penetrant molecular glue (MG) degraders. Distinct from Proteolysis Targeting Chimeras (PROTACs) that require a high- affinity ligand for the target protein, molecular glues can mediate degradation by engaging specific protein surface features, such as loops, without the necessity of a dedicated binder. These degraders aim to induce the proteasomal degradation of VAV1, thereby ablating both its enzymatic and scaffolding functions, which are implicated in neuroinflammation. The research strategy involves three primary aims: 1) To optimize lead VAV1 molecular glue degraders for enhanced potency, brain penetration, and favorable pharmacokinetic properties using advanced computational modeling and medicinal chemistry. 2) To evaluate the in vivo efficacy of the optimized VAV1 degraders in preclinical mouse models of MS (Experimental Autoimmune Encephalomyelitis - EAE), assessing their ability to ameliorate disease severity, reduce CNS inflammation and demyelination, and engage VAV1 in the CNS. 3) To investigate the Structure-Activity Relationship (SAR) of a novel non-canonical VAV1 degron motif, aiming to expand the understanding of molecular glue-mediated degradation and enable the rational design of degraders for other challenging therapeutic targets. Successful completion of this project is expected to deliver preclinical candidate VAV1 degraders with the potential for a novel, effective, and safer treatment paradigm for MS. Furthermore, the insights gained into non-canonical degron recognition will significantly advance the field of targeted protein degradation, broadening the scope of "undruggable" targets for therapeutic intervention in various diseases.

From B-cell decisions to antibody repertoires

PROJECT SUMMARY/ABSTRACT Vaccine responses are highly variable across the population and not without risk for debilitating side-effects. Antibody-mediated immunity is generated by a Darwinian process to generate B-cells that contain B-cell receptors (BCR) that have high affinity for the pathogen-derived antigen, while also eliminating B-cells that happen to react to self-antigens. This process depends on cell fate decisions such as (i) death vs survival, (ii) entry into a proliferative program, (iii) differentiation into antibody-secreting plasma cells. According to clonal selection theory, B-cell fate decisions are made based on the genetically encoded affinity of the the BCR to the antigen (Signal 1) and the cognate T-cells’ TCR to the antigen peptide (Signal 2). However, single-cell resolution studies have revealed that fate decisions of genetically identical B-cells are remarkably heterogeneous. Our studies of the previous funding period revealed that B-cell epigenetic heterogeneity is in fact dynamically controlled: it is generated during the selection process but remains largely stable during the proliferative burst. This leads to our newly proposed Aim 1 to examine how the dynamic control of epigenetic state variability affects antibody responses. An innovative multi-scale model of Darwinian evolution directs and interprets experimental studies by life cell video microscopy in vitro and in immunization studies in vivo. Our previous studies also found that B-cells are capable of sensing the time gap between signal 1 and 2, suggesting a temporal proofreading mechanism for negative selection. This leads to newly proposed Aim 2 which seeks to identify the regulatory circuits that control the stringency of negative selection, as well as contextual germinal center (GC) cytokines that could be manipulable in vivo. These in silico and in vitro studies are followed by in vivo immunization to extend their physiological relevance. Finally, in Aim 3, we will ask what determines the time-gap of signal1 and signal 2, which occur in the immune- induced structure of the GC. We will develop a new model that simulates B-cell fate decisions as a function of their interactions with antigen-presenting stromal cells and T-cells that may be cognate or non-cognate. Model simulations will be used to interpret spatial transcriptomic data to test different adjuvants and predictions will be tested in in vivo immunization studies. With mouse models of inflammation and aging we will examine how adjuvants alter vaccine efficacy and risk.

Borrelia burgdorferi genotypic diversity, pathogenesis, and host cellular responses

PROJECT SUMMARY Lyme disease is the most common tick-borne illness in the United States, with an estimated 476,000 cases annually, and Pennsylvania (PA) consistently reports one of the highest case numbers nationwide. Borrelia burgdorferi sensu stricto (Bb) is a causative agent of Lyme disease in the US and is transmitted by Ixodes spp. ticks. Bb produces various outer surface proteins (Osp) and other mechanisms to survive in vectors, evade host immune systems, and to propagate infection within a host. Over 35 OspC genotypes have been characterized, which fluctuate in abundance in natural vector and host populations, suggesting host adaptation. While many Lyme-infected patients recover following antibiotic treatment, some may experience neurological symptoms, Lyme neuroborreliosis (LNB), which may be associated with specific genotypes. While previous studies focused on clinical manifestations, pathogenicity, genetic variations, and host immune responses using mouse models or patient samples, the genotype-specific immune responses that contribute to disease progression in humans remain poorly understood. Our central hypothesis is that certain Bb OspC genotypes, maintained in natural populations, are associated with distinct host immune responses that influence disease severity, progression, and persistence. Aim 1 will define the dynamics of OspC genotypes in tick and small mammal populations over time in Western PA to establish a 16-year longitudinal tick study and an 8-year longitudinal small mammal study. Using deep amplicon sequencing, we will quantify genotype diversity, detect low-abundance genotypes, and identify potential host-adapted genotypes. These empirical data will inform a compartmental mathematical model to evaluate OspC genotype prevalence, distribution, and public health risks, including LNB, across space and time. Aim 2 will assess how distinct Bb OspC genotypes affect the host immune landscape and cellular responses using human samples. To determine how Bb genotype contributes to disease phenotype, we will perform immune profiling studies which will include microscopy-based assessment of infected cell cultures, flow cytometric analysis of immune cell phenotypes, and measurement of genotype-specific cytokine, chemokine, and antigen production (sub-Aim2a). We will also employ multi-omics approaches that integrate single cell RNA sequencing with antibody-based protein profiling (scRNA-seq/Ab-seq) to characterize transcriptional and functional changes in immune cell populations exposed to different Bb genotypes (sub-Aim2b). This work is innovative in its integration of long-term ecological data with advanced immune profiling and single cell multi- omics to uncover genotype-specific mechanisms of Bb pathogenicity and human immune response—an approach not previously applied in Lyme disease research. These studies will clarify how specific genotypes influence immune responses and disease severity. Together, the proposed aims will identify critical genetic and immunological mechanisms that drive Bb pathogenicity and human susceptibility, informing the development of improved diagnostics, targeted therapies, and public health interventions to reduce the burden of Lyme disease.

Th17 plasticity in rheumatoid arthritis

ABSTRACT The objective of this grant application is to explore the plasticity of Th17 in arthritis. Interleukin-17A (IL-17A) producing Th17 are present in the blood and synovium of patients with rheumatoid arthritis (RA). However, targeting of IL17A has been insufficient to control joint inflammation of RA patients. One potential scenario is that in the context of worsening RA joint inflammation, Th17 undergo conversion into pathogenic IL17A- negative cell populations, collectively called exTh17. The conversion of Th17 into exTh17 has been documented in the context of neuroinflammation, colitis, and infection. However, the occurrence of Th17 plasticity in autoimmune arthritis and its potential role in perpetuating synovial inflammation has remained mostly unexplored. We generated a novel fate-mapping mouse model of autoimmune arthritis, which allows to follow the conversion of Th17 into exTh17, and collected preliminary data suggesting that Th17 undergo significant loss of IL17A expression and conversion into exTh17 in the context of synovial inflammation. We also identified exTh17 signatures which might help exTh17 perpetuate joint inflammation despite their loss of IL17A expression. Here our objective is to further elucidate intrinsic (Aim 1) and extrinsic (Aim 2) mechanism of Th17-exTh17 conversion and exTh17-mediated joint inflammation, and explore the potential role of exTh17 in RA interstitial lung disease (ILD, Aim 3) a feared and often untreatable complication of established RA. Our long-term goal is to leverage the knowledge of local immune cell phenotypes and how they change at various stages of disease to enable stage-specific and personalized therapies of RA which minimize non- specific immunosuppression.

Regulation of neutrophil endoplasmic reticulum stress response by IRE1a

Project Summary/Abstract: The lungs are exposed to pathogens and environmental toxins that trigger stress and cause numerous respiratory diseases. Effective host defenses against lung infection by bacterial pathogens, including methicillin- resistant Staphylococcus aureus (MRSA), rely on innate immune cells including neutrophils, prominent early responders to sites of infection. If host defenses are ineffective, MRSA causes serious lung infection, resulting in severe morbidity and a significant economic burden on healthcare facilities, where it is endemic. MRSA infections have a mortality rate of up to 14% and an estimated $500 million in healthcare costs in the US alone. Increasing resistance to vancomycin, the last resort antibiotic for MRSA infections, underscore the urgent need for innovative treatment approaches. Although directly targeting pathogens with antibiotics has been a successful approach for treating infections, many pathogens, including MRSA, eventually will become resistant to these drugs. As an alternative, immunomodulatory strategies to enhance host defenses, such as those shown to be effective against cancer cells, have the potential for treating drug-resistant pathogen infections. Recently, we showed that the inositol-requiring enzyme 1-α (IRE1α), an endoplasmic reticulum (ER) stress sensor, is required for clearance of MRSA in a murine skin abscess model, where neutrophils are robustly recruited to the site of infection. Further, IRE1α coordinates signaling events upstream of calcium (Ca2+) mobilization, histone citrullination, and production of mitochondrial reactive oxygen species (mitoROS), all of which are important for neutrophil inflammatory responses including the formation of antimicrobial neutrophil extracellular traps (NETs). Because excessive neutrophil activation and NET release can be detrimental to vital organs, it is not clear whether neutrophil IRE1α-mediated stress responses aid or impede the resolution of infection in the lungs. While IRE1α activation has been linked to the development of lung fibrosis through the regulation of alveolar epithelial- to-mesenchymal transition in the context of chronic inflammatory diseases, its role in pulmonary neutrophil defenses is unknown. Thus, there is a gap in our knowledge of how cellular stress responses modulate pulmonary neutrophil defenses and infection outcomes in the lungs. The overarching goal of this proposal is to elucidate the mechanisms by which neutrophil IRE1α signaling influences production of mitoROS and Ca2+ mobilization to drive NET release, injure lungs, and regulate pulmonary host defense against MRSA. We will accomplish the following Aims: (1) Define the molecular mechanisms underlying IRE1α-mediated mitoROS hyperactivation of human and mouse primary neutrophils and excessive NET release, and (2) Elucidate the role of neutrophil IRE1α signaling in excessive NET release, lung injury, and immunity in vivo using a MRSA pneumonia infection mouse model. These studies will yield mechanistic insight into how IRE1α-driven ER stress responses impact pulmonary neutrophil defenses and lung injury revealing potential targets for anti-microbial immunotherapies.

Mechanisms of antigen-specific T cell activation in MOGAD

PROJECT SUMMARY / ABSTRACT The overarching goal of this application is to train Dr. Carson E. Moseley, MD, PhD, who is a clinical neurologist and a research immunologist, to become an independent investigator studying and treating neuroimmunologic disorders. Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) is a recently described, severe, neuroinflammatory syndrome of the central nervous system (CNS) with no approved therapies. Although MOG-specific antibodies helped define the disease, MOG antibodies alone are not clearly pathogenic and our understanding of MOGAD immunopathology is limited. CD4+ T cells are a dominant lymphocyte population in MOGAD lesions, yet the targets of T cell responses to MOG and how T and B cells interact to drive pathogenic immune response in MOGAD are unknown. This proposal uses a complementary approach of human and mouse immunology along with new technologies in T cell repertoire mapping and genome editing to dissect MOG-specific CD4+ T cell responses in MOGAD. Additionally, it will use new models to investigate how B cells promote pathogenic T cell differentiation and select pathogenic T cell receptors. The proposed training plan involves mentored training, seminars, formal learning, and advising to ensure completion of the proposed research and Dr. Moseley’s career development. He will train at UCSF, which is an outstanding institute for research and environment for physician-scientists. He will receive training in human immunology and CRISPR-based gene editing technologies. He will be mentored by Dr. Scott Zamvil, a leader in identifying antigen-specific T cell responses in neuroimmunologic disorders, and co-mentored by Dr. Alexander Marson, an expert in CRISPR gene editing to understand lymphocyte function. This application will provide Dr. Moseley with the long-term skills needed to become an independent investigator leading efforts to study and treat neuroimmunologic disorders.

Investigating the nonlinear complex dynamics of the tuft cell-microbiome cross-talk: the impact of feedback loops on immune regulation, microbial modulation and response to tissue insults

Project Abstract Tuft cells (TCs) are specialized chemosensory epithelial cells that are emerging as critical regulators of intestinal homeostasis. Named over 70 years ago based on their distinct morphology, a defined function for TCs was only elucidated in the last decade. TCs in the small intestine sense succinate from helminths to initiate type 2 immune responses that mediate parasite expulsion. Recently, we discovered a novel physiologic function for TCs in the colon, where their role had been considered minimal. Succinate, a key microbial metabolite, is produced by colonic microbiota as both a precursor to other metabolites and a cross-feeding fuel source for pathogens. TCs respond to succinate by secreting interleukin-25 (IL-25), which activates type 2 cytokine- producing lymphocytes (T2Ls), amplifying TC expansion and reinforcing barrier function. We recently demonstrated that this SPB–TC–IL-25–T2L feedback loop is essential for protection against pathogen-induced colitis. Our preliminary data further suggest that TCs actively promote colonization by succinate-producing bacteria (SPBs), establishing positive feedback on TC-supporting microbes, while other epithelial cells such as goblet cells (GCs) and Paneth cells (PCs) may exert complementary or counterbalancing influences. Supported by new modeling insights, we hypothesize that these epithelial–immune–microbiome interactions form coordinated feedback loops that collectively optimize intestinal resilience. These loops may create a dynamic, multi-stable system that flexibly transitions between homeostatic and hyperplastic states, buffering against microbial fluctuations and pathogenic insults while preventing uncontrolled type 2 inflammation. Using a combination of mathematical modeling and experimental validation, we will develop a multi- layered systems framework to explore how epithelial–immune–microbial feedbacks shape resilience or breakdown in clinically relevant models of colonic infection and inflammation. Our three Aims will (1) develop, calibrate, and validate a mathematical model that integrates TCs, GCs, PCs, SPBs, and SCBs; (2) define the immunological circuits governing epithelial–microbiome equilibrium; and (3) determine how epithelial feedbacks regulate microbial community structure and resilience. In line with NIH’s new initiative to prioritize human-based research, our proposal combines computational modeling, human colonic organoids, and complementary mouse models. Organoid experiments will provide human-relevant data for model calibration, while in vivo studies validate systemic predictions, ensuring both rigor and translational relevance while minimizing reliance on animal models. This work will generate interoperable models that integrate epithelial, microbial, and immune networks, providing predictive insight into intestinal outcomes under homeostatic, infectious, and inflammatory conditions and informing therapeutic strategies for microbiome-targeted interventions.

Circadian regulation of reperfusion efficacy in acute ischemic stroke

Reperfusion with thrombectomy has changed the clinical landscape for ischemic stroke. Recently, some studies suggest that patients with “large cores” may still benefit from reperfusion. Why? If these “cores” represent dead brain, why should reperfusion help? One logical explanation is that currently used neuroimaging “cores”, do not always identify uniformly dead tissue. Our pilot data suggest that these “cores” include tissue with a wide range of injury, indicated as changes in relative CT Hounsfield Units (rHU). Importantly, circadian mechanisms may be involved. Ischemic tissue with less severe changes in rHU tend to occur in the morning (active phase) when responses to reperfusion are better. In mouse models of stroke, ischemic injury is also less severe when strokes occur during the nighttime (active phase for nocturnal animals). In contrast, more severe ischemic injury during the daytime (inactive phase for mice) is accompanied by dampened vasodilation and CBF response along with increased immunothrombosis and neutrophil extracellular traps (NETosis). Is it possible that understanding these circadian mechanisms may help identify patients who respond best to reperfusion? And is it possible that targeting these circadian mechanisms can help convert non- responders into responders? In this multi-PI project, we use a translational approach (clinical neuroimaging and biomarkers in stroke patients, mouse models of stroke, CT-PET imaging of tissue viability, molecular pharmacology) with three integrated aims that can be pursued in parallel. Aim 1 will use neuroimaging in stroke patients to show that less severe rHU values in reperfusion-responsive “cores” tend to occur in the morning, whereas more severe rHU values in reperfusion-non-responsive “cores” occur later. Aim 2 will use clinical biomarkers to show that more severe rHU “cores” that are not reperfusion-responsive correlate with circadian effects on vasodilation and immunothrombosis. Aim 3 will use mouse stroke models to test whether targeting these circadian mechanisms of vasodilation and immunothrombosis can convert reperfusion-non-responders into reperfusion-responders. Patients cannot choose when they have a stroke. So why should we pay attention to circadian mechanisms? There may be 2 reasons that are addressed by the present project. First, thrombectomy is resource-intensive, and in spite of the very low number-needed-to-treat, only 20% of “large core” patients do well after reperfusion. Our studies may help identify who (when) these responders are. Second, the pathophysiologic mechanisms of cerebral ischemia differ depending on time-of-day. Therefore, understanding and then targeting these circadian mechanisms may allow us to convert reperfusion non-responders into responders.

Circulating extracellular vesicles as functional indicators of maternal mental and physical health in pregnancy and postpartum

Women with high levels of adverse childhood experiences (ACEs) are at significantly greater risk for negative health outcomes in pregnancy and postpartum, including gestational diabetes, PTB, and depressed mood. However, we still lack biomarkers or a sufficient understanding of causal mechanisms. Extracellular vesicles (EVs) are one of the most dynamic and abundant biological signals secreted into maternal circulation, largely produced by the placenta – where levels increase 4-5-fold during pregnancy. Similarly, removal of the placenta at delivery produces a dramatic drop in maternal EV concentration. Across species, we and others have identified significant EV changes during pregnancy associated with homeostatic regulation, including glucose and glucocorticoid levels, supporting key roles for EVs in maternal health. However, longitudinal studies in human pregnancy and postpartum have not been conducted. We know little as to the mechanisms controlling EV secretion or the roles for EVs in maternal pregnancy and postpartum health. Our decade’s long work identified the X-linked gene, O-glycosyltransferase (OGT), in mouse and human placenta as a master gage of the maternal milieu, where OGT regulation of annexin A1 (AA1) is key to EV cargo loading and secretion from the placenta. We recently reported that placental OGT levels positively correlate with maternal EV concentration. How this association may contribute toward postpartum health, including regulating maternal stress physiology and mood in humans is not known. We hypothesize that increased ACEs, similar to stress in preclinical models, are negatively associated with a cell’s ability to secrete EVs important to maintain homeostasis in the face of the challenges of pregnancy and postpartum, producing an increasingly unhealthy state. Therefore, the goals of these proposed studies in both mice and humans are as follows: 1) To identify cellular mechanisms involved in EV secretion important to maternal health outcomes utilizing the placenta as a tool to genetically target OGT in mice and examine maternal homeostatic control related to EV concentration and composition during pregnancy; 2) To examine the functional ability for a dynamic elevation in maternal EV concentration to improve homeostatic regulation in pregnancy and postpartum using chemogenetic activation (DREADDs) of placenta trophoblast cells in pregnancy, and by EV transfer by tail vein injection postpartum; and 3) To examine in women changes in maternal EVs in a longitudinal pregnancy and postpartum study in association with maternal glucose and cortisol changes, we will examine markers of physical (glucose challenge test), HPA stress (hair cortisol & stress- stimulated salivary cortisol) and psychological (Hamilton Rating Scale for Depression, Perceived Stress Scale) health across pregnancy and the postpartum period in 150 healthy women with varying degrees of exposure to ACEs as measured using the ACE Questionnaire (ACE-Q).

Hepatotoxicity of Legacy and Replacement PFAS: Role of BRUCE-Mitochondrial Interactions

Epidemiological studies have shown a strong association between exposure to PFAS (Per- and Poly- fluoroalkyl Substances) and liver toxicity. Particularly, legacy C8-PFAS members, PFOS (perfluorooctane sulfonate) and PFOA (perfluorooctanoic acid), are highly toxic, with PFOS estimated to be approximately 10 times more toxic than PFOA in ecotoxicity models. Consequently, PFAS replacements such as GenX and PFBS are marketed as safe alternatives, although growing evidence indicates that these substitutes also exhibit toxic effects. Lab animal model studies have shown hepatotoxic effects of both legacy and replacement PFAS members, characterized by Metabolic dysfunction-associated steatotic liver disease (MASLD) and its severe form Metabolic dysfunction- associated steatohepatitis (MASH), the two chronic liver diseases affecting an estimated 80-100 million Americans. The broader objective of this project is to understand the underlying mechanisms of PFAS hepatotoxicity in MASLD/MASH. In this context, our initial studies have shown that PFAS exposure of mice downregulates hepatic BRUCE, an autophagy inhibitor, resulting in development of MASLD in WT, and more severe MASLD and even progression to MASH in BRUCE liver-knockdown (BKO) mice. Using primary hepatocytes, we found PFAS-induced BRUCE reduction compromised mitochondrial (mt) functions (respiration, fatty acid oxidation/FAO, and ATP production) and suppressed mitophagy in WT and more so in BKO mice. Pharmacological restoration of mt function in mice prevented PFAS-induced MASLD/MASH. Guided by these compelling preliminary data and scientific premise, we hypothesize that PFAS degradation of BRUCE in hepatocytes induces excessive autophagy (resulting in cytotoxicity) and inhibits mitophagy (resulting in accumulation of damaged mitochondria), leading to release of mtDAMPs to activate inflammation/ fibrosis, thereby facilitating progression from MASLD to MASH. We will test this by three specific aims. Aim 1 (ex vivo) is to determine the human-relevant PFAS doses that modulate BRUCE levels for homeostatic vs cytotoxic autophagy and how BRUCE in turn regulates autophagy. Aim 2 (ex vivo) will investigate BRUCE-driven mitophagy pathway specific to PFAS exposure at human-relevant doses. Aim 3 (ex vivo and in vivo) will involve ex vivo simulation experiments to characterize the role of PFAS-induced, BRUCE-dependent hepatocyte- released mt DAMPs in activation of immune and fibrogenic cells using co-culture assays. Next, we will perform in vivo intervention to validate the role of PFAS-damaged mitochondria in driving MASH progression in mouse models. Furthermore, human relevance of the delineated mechanisms will be ascertained and validated using iPSC-derived human liver organoid system. Impact: This project will advance our understanding of autophagy/mitophagy-centric mechanisms with therapeutic potential in the context of PFAS-induced liver disease MASLD/MASH.

Protective efficacy and immunogenicity of a live attenuated Chlamydia strain

PROJECT SUMMARY The main goal of this project is to rigorously evaluate the immunogenicity and protective efficacy of a mutant, live attenuated Chlamydia trachomatis (CT) vaccine strain in an established nonhuman primate (NHP) model that accurately mimics many aspects of human CT infection. This work is highly significant, as CT is the leading cause of bacterial sexually transmitted infection and an important causative agent of morbidity in women. Although the development of an effective CT vaccine is an urgent medical priority, no approved vaccines exist and it is imperative to pursue new candidates. Historical evidence supports the vaccine efficacy of whole Chlamydia organisms in protecting the reproductive tract from reinfection, primarily using C. muridarum infections in a mouse model. Recent advances in Chlamydia genetic engineering now allow for the development of genetically attenuated strains which can be evaluated as live vaccines in preclinical models. We recently characterized a human-tropic CT mutant with a disruption in garD (CT∆garD); this mutant is sensitive to an intracellular, IFNγ activated defense mechanism and we demonstrated that this strain was attenuated in the female NHP genital tract. In a pilot vaccine efficacy study, we further demonstrated that immunization of macaques with CT∆garD was safe and elicited protection against subsequent challenge with wildtype CT. A unique feature of this strain is that it arrests at an intracellular stage and thus presents a broad array of desirable T and B cell antigens that are broadly conserved across circulating CT strains. We will first generate an improved genetically attenuated CT strain that harbors a clean deletion of garD, and we will subsequently genetically and phenotypically validate its attenuation phenotype. We will then conduct an immunogenicity and efficacy study in female macaques to determine the optimal dosing regimen of live attenuated CT for eliciting protective cellular and humoral immune responses, and also protective efficacy, against challenge with a wild type circulating clinical CT strain. These studies will investigate the potential for a live attenuated human tropic vaccine candidate in a macaque preclinical model and pave the way for greater understanding of immune correlates of protection against CT.

Tbx4-Driven Pulmonary Hypertension: Mechanisms and Therapeutic Targets

Project Summary: Heterozygous rare variants in TBX4 are the second most common cause of heritable pulmonary arterial hypertension (PAH). Presentation of this form is commonly in children. Patients with mutations in TBX4 generally have alveolar simplification or hypoplasia in addition to elevated pulmonary vascular resistance. We have developed a set of three tools to help determine the molecular etiology of TBX4-induced PAH; (1) we identified the direct binding targets using a combination of ChIP-seq and RNA-seq; (2) we developed a mouse model with Tbx4 knockout after birth, that substantially phenocopies human disease; (3) we performed single-cell RNA-seq on these mice. By combining these three tools, we can develop a complete model for how loss of a transcription factor leads to the molecular and physiologic changes we see in our mice. The phenotype in mice appears to be dominated by defects in pericytes, resulting in impaired angiogenesis. Pericytes, which strongly express Tbx4, are cells located on the outside of capillaries and precapillary arterioles, and can either stabilize vessels (mesh pericytes), or drive angiogenesis (angiogenic pericytes). The pericytes in Tbx4 mutant mice are heavily skewed towards mesh and away from the angiogenic phenotype. Loss of Tbx4 results in derepression of Tbx4 binding target Rgs5 (10x induction), which directly results in inhibition of Pi3K, and the phenotypic switch in pericytes. We will test this hypothesis through pericyte-specific Tbx4 knockout (Aim 1) and pharmacologic induction of Pi3K in vivo in prevention and rescue models, as well as by siRNA to Rgs5 in precision-cut lung slices from Tbx4 KO mice (Aim 3). We will also test the role of Tbx4 in fibroblasts and smooth muscle using cell-specific knockouts – based on our mouse and single cell data, we expect they contribute somewhat, but primarily through increased stiffness (Aim 2). Finally, we will confirm relevance to human disease through spatial transcriptomics in lung sections explanted from patients with TBX4 mutation or rearrangement (Aim 1), and through determining whether defects in human patient iPSC-derived pericytes can be corrected through Rgs5 or Pi3K interventions (Aim 3). In combination, these aims determine the cellular and molecular mechanisms leading from mutation to physiology with loss of TBX4, and establish therapeutic targets.

Mechanisms of age-related inflammatory dysregulation in the pathogenesis of periodontal disease

Periodontal disease is a chronic inflammatory condition that affects the supporting tissues of the dentition. Similar to other chronic inflammatory conditions, the prevalence of periodontal disease increases with age. Dysregulation of the host inflammatory response is central to the pathogenesis of periodontal disease and other age-related diseases. Therefore, an improved understanding of the pathologic mechanisms that contribute to age-related inflammatory dysregulation is needed to better manage periodontal disease in older adults. Towards understanding a mechanism of age-related inflammatory dysregulation in periodontal disease, we will investigate the role of triggering receptor expressed on myeloid cells 2 (TREM2). TREM2 is a potent immunoregulator expressed on macrophages. Signaling through TREM2 downregulates inflammation, in part, through inhibition of inflammatory cytokine expression. Dysregulation of TREM2 has been implicated in chronic inflammatory disease and age-related conditions, such as Alzheimer’s disease, liver disease, and osteoarthritis. However, the role of TREM2 in periodontal disease is understudied. Therefore, we propose to study TREM2 in the pathogenesis of periodontal disease and age-related inflammatory dysregulation. Our preliminary work has demonstrated that TREM2 is critical in macrophage immunoregulatory processes in the periodontium and TREM2 dysregulation contributes to periodontal disease in mice. We have shown that Trem2 is expressed in macrophages isolated form the periodontium in mice. We demonstrated that old mice expressed less Trem2 in the periodontium compared to young, which was associated with local inflammatory dysregulation and increased periodontal disease severity. Interestingly, Trem2 depletion in young mice resulted in increased inflammatory dysregulation and periodontal disease severity, similar to what is observed in old mice. From the preliminary data, we hypothesize that TREM2 modulates macrophage activity in the periodontium and age-related dysregulation of TREM2 drives a pathologic inflammatory response in periodontal disease. In Aim 1, we will demonstrate the extent to which TREM2 modulates inflammation and periodontal disease severity using old, young, and Trem2-/- mouse models of periodontal disease. In Aim 2, we will develop tissue-specific, single cell map of the immune cells in the periodontium and understand the effect of age and Trem2 on immune cell phenotypes and subpopulations. Findings from this proposal will elucidate a novel mechanism in age-related inflammatory dysregulation in the pathogenesis of periodontal disease and further advance our understanding of the role of TREM2 within oral tissues. This proposal was designed to generate a novel body of work that will be used to develop the independent research program of an early stage investigator and to support an R01 proposal to be submitted at the completion of this project period.

Intrinsic and extrinsic mechanisms underlying trigeminal nerve deficits in familial dysautonomia

PROJECT SUMMARY Rare diseases impose a significant burden on the US healthcare system, accounting for nearly half of all expenditures for their treatment. This statistic alone supports the need to invest in research to develop therapeutic interventions for rare diseases since the economic benefit outweighs the continued expense of financial resources. Familial dysautonomia (FD) is a rare, hereditary disease that arises from a splice site mutation in Elongator acetyltransferase complex subunit 1 (ELP1) and impacts the nervous system. To date, FD patients continue to face life-threatening complications involving basic involuntary functions like swallowing and somatosensation because there is no cure for this ultimately fatal neuropathy. FD patients exhibit symptoms due to defects in their somatosensory trigeminal nerves, whose cell bodies reside in the trigeminal ganglion (TG) and are derived from neural crest and placode cells. Recent studies from our lab using an FD mouse model (Elp1 deleted from neural crest cells) revealed TG axon outgrowth and target tissue innervation deficits, recapitulating phenotypes observed in FD patients. However, the mechanisms by which Elp1 mediates normal TG development, and how this goes awry in FD, remain largely elusive. To gain insight into Elp1 function, we performed mass spectrometry to evaluate the TG proteome of normal and FD mouse embryos. Our results uncovered statistically significant increases in extracellular matrix (ECM) and ECM binding proteins, pointing to altered TG biomechanical properties and, more broadly, changes in mechanotransduction, the process by which cells translate extrinsic cues into intrinsic signaling pathways that modulate gene expression. Importantly, proper axon outgrowth relies upon mechanotransduction as growth cones on axons sense and respond to their environment. In the head, this environment consists of ECM and cranial mesenchyme cells, but the impact of Elp1 loss from the latter is not known, including the potential for altered tissue biomechanics that could influence TG axon outgrowth. We hypothesize that loss of Elp1 induces changes in the biomechanical properties of both the TG/nerves and ECM/cranial mesenchyme, modifying mechanotransduction and leading to TG defects in FD, which we will interrogate in the following Specific Aims: 1) define the biomechanical properties of the TG/nerves and ECM/cranial mesenchyme and 2) determine the role of cranial mesenchyme Elp1 in mediating proper TG axon outgrowth. Our innovative research proposal takes a systems-level, multidisciplinary approach involving embryology, biomechanics, and high-resolution microscopy, with the goal of integrating molecular, cellular, and tissue data. These results will significantly advance our knowledge of the molecular mechanisms underscoring TG development and, collectively, inform treatment strategies for birth defects or disorders like FD with TG dysfunction, as well as nerve repair and/or regeneration after injury or disease.

Directing the Evolution of Common Human Precursors into HIV-1 Broadly Neutralizing Antibodies

Project Summary An effective HIV vaccine will likely elicit broadly neutralizing antibodies (bnAbs). Doing so, however, remains a major challenge because bnAbs usually require multiple rare and unusual changes that emerge after years of active infection. It is not clear that a practical number of immunizations can consistently recapitulate this process. Although investigators have successfully expanded defined precursors of known bnAbs, they have not moved these diversified precursors to a specific target in humans. Importantly here, the severity of this problem increases rapidly with the number changes needed. The problem further deepens if the required changes are in slow-to-mutate antibody framework regions or require specific indels. The need to move from precursor to bnAb in the fewest steps motivates our focus on the V2 apex epitope of the HIV-1 envelope glycoprotein (Env). Apex bnAbs are qualitatively different from other bnAb classes. They require far fewer mutations, located in their rapidly evolving heavy-chain CDR3 (HCDR3) regions. These HCDR3s are unusually important to their ability to neutralize virus. For example, we have shown that a diverse repertoire of mouse B cell receptors can be modified with apex bnAb HCDR3s, and the resulting mouse B cells generated potent neutralizing sera. Thus, apex precursors can largely be defined by their HCDR3s alone and are far more common than other defined bnAb precursors. Interestingly, these HCDR3 are very similar to those of another class of antibodies that recognize the CD4-induced co-receptor-binding site (CoRBS). Both antibody classes have unusually long HCDR3s with sulfated tyrosines at their tips. Unlike apex bnAbs, these non-neutralizing CoRBS antibodies are readily elicited through vaccination. We have recently shown that apex precursors also bind the CoRBS, suggesting that some apex bnAbs emerge from CoRBS antibodies. Thus, the first step of sequential vaccine strategies, expanding and diversifying a defined precursor pool, is straightforward. Here we divide the remaining goals into two: moving from a precursor that does not bind Env to one that does so and then broaden it to recognize the majority of circulating isolates. We have already made significant progress in the first step: we have shown in our original mouse vaccine model that we can generate potent apex- specific neutralizing antisera. However the breadth of this sera remains limited. Building on these studies, we will pursue three goals: (1) Define the essential mutations that transform a CoRBS antibody into one that binds the Env apex and then generate antigens that select for these mutations. (2) Define mutations and generate antigens that expand the breadth of these antibodies, transforming them to bnAbs, and (3) Evaluate these antigens in a novel system that models key features of the human apex response in mice, and iteratively refine this process using antibodies and HCDR3s drawn from a wide panel of HIV-naïve persons. In short, these studies develop original concepts and tools that can accelerate development of an HIV-1 vaccine and deepen our understanding of the antibody response to vaccines and pathogens.

A NOVEL GEMM TO ELUCIDATE THE ROLE OF CHAF1A IN NEUROBLASTOMA DEVELOPMENT

PROJECT SUMMARY: This proposal focuses on the fundamental understanding on how the CHAF1A oncogene drives molecular mechanisms, cellular signaling, and metabolic processes in the oncogenesis of neuroblastoma (NB). NB is an aggressive pediatric cancer, which accounts for 15% of pediatric cancer mortalities. High-risk NB is thought to arise from a small number of recurrent genetic alterations that block the ability of neural crest cells (NCCs) to differentiate. To assess the molecular mechanisms governing NC differentiation, our laboratory has established a definitive role of the epigenetic regulator CHAF1A in blocking NC differentiation and driving NB oncogenesis. In this proposal, we will determine the impact of CHAF1A on NB initiation and progression. To accomplish this goal, we propose to develop a novel CHAF1A-driven genetically-engineered mouse model (GEMM) of NB and test the impact of CHAF1A on NB incidence, histology and metastasis, and the tumor immune microenvironment (TIME). We hypothesize that CHAF1A will increase de novo incidence of NB, reduce mouse survival, and promote a suppressive TIME. By developing a novel GEMM of NB and employing innovative technology (including ATAC-seq, lipidomics, and scRNA-seq), we will: 1- elucidate the role of CHAF1A in NB tumor initiation and progression; and 2- determine the impact of CHAF1A on MYCN-induced oncogenesis. These findings will provide a novel view on the molecular mechanisms driving NB initiation, and will have high clinical implications, informing future differentiation-based interventions for high-risk NBs.

Pathogenic mechanisms of expanded ZFHX3 in SCA4 cerebellar organoids

Spinocerebellar ataxia type 4 (SCA4) is a disabling neurodegenerative disease characterized by progressive cerebellar ataxia, and the causative GGC-repeat expansion in ZFHX3 (ZHFX3-exp) was just discovered this year by our lab and others. Our research aims to understand how ZFHX3-exp causes SCA4 and to identify molecular therapeutic targets that can be quickly advanced into clinical trials. SCA4 is one of the four poly-glycine diseases that share the presence of neuronal intranuclear inclusion (NIIs) as a disease hallmark. In SCA4, NIIs are positive for ZFHX3, p62 and ubiquitin, indicating the loss of proteostasis as a mechanism of neurodegeneration. In addition, ZFHX3 RNA-gain-of-function may also contribute to neurodegeneration. Beyond this, knowledge of the disease mechanisms that underly SCA4 is extremely limited and there are currently no disease-modifying treatments for SCA4 or other polyG/NII diseases. There are no SCA4 mouse models and because of the high GC content in the repeat expansion complicates the production of SCA4 mouse models. We propose a novel approach to characterizing SCA4 Purkinje cell (PC) pathogenesis using human cerebellar organoids. Our approach allows for rapidly advancing the understanding of the pathogenesis and potential treatments of SCA4. Using cerebellar organoids will enable investigation on functional PCs, cerebellar neurodegeneration and the testing of potential therapeutic strategies. In aim 1, we will generate cerebellar organoids from five SCA4 patient-derived iPSC lines, and normal control iPSCs from individuals of the same family. These iPSC lines are already established in our laboratory. In aim 2, we will investigate PC viability, NII protein composition, proteostasis pathways, RNA gain-of-function and cell-type-specific dysregulated pathways by single nucleus RNA sequencing. In addition, we will study potential therapeutic targets by lentiviral knockdown and single nucleus RNA sequencing. SCA4 patient iPSCs express overabundant STAU1 and ATXN2. We will evaluate how lowering the abundance of these proteins modifies the PC molecular phenotype. Together, these experiments will establish a model to greatly enhance the understanding of human PC neurodegeneration, the pathological mechanisms of SCA4 and possible avenues of treatment.

Programming Offspring Metabolism: The Role of Milk Extracellular Vesicles in Fat Development

SUMMARY Obesity is a global health crisis, contributing significantly to the prevalence of metabolic disorders, cardiovascular diseases, and various chronic conditions. A growing body of evidence suggests that maternal obesity during pregnancy and lactation can predispose offspring to obesity and metabolic dysfunction later in life. However, the mechanisms by which maternal obesity programs these adverse outcomes in offspring remain poorly understood. Breast milk is not only a source of essential nutrients but also contains bioactive components, including extracellular vesicles (EVs), which play crucial roles in cellular communication and development. Recent studies have shown that EVs can survive digestion and enter the infant’s circulation, influencing immune and metabolic development. Despite the established link between maternal obesity and altered breast milk composition, no study has investigated the role of milk-derived EVs (mEVs) in programming offspring fat development and metabolism. Understanding this novel pathway could revolutionize our approach to preventing intergenerational transmission of obesity. Our preliminary studies using a mouse model of maternal high-fat diet-induced obesity revealed significant alterations in mEV biogenesis and cargo composition, including changes in specific miRNAs. Oral administration of mEVs from obese dams to neonatal mice increased adiposity and impaired lipid metabolism, indicating that mEVs are crucial in modulating fat development and metabolic pathways in offspring. Several key miRNAs found in mouse mEVs are conserved in human milk EVs, highlighting the potential translational relevance of our findings to human health. We hypothesize that mEVs are critical mediators of maternal obesity’s programming effects on offspring metabolism and adiposity. In specific aim 1, we will use mouse models and advanced molecular techniques (miRNA sequencing, proteomics, and lipidomics) to characterize how maternal obesity affects mEV biogenesis and the composition of their bioactive cargo. We will also evaluate how maternal dietary intake, independent of obesity, influences mEV composition. Specific aim 2 will define the programming effects of mEVs on offspring energy metabolism and obesity. In addition, we will explore whether human milk EVs from lean and obese mothers exert similar programming effects on fat development and metabolism in a mouse model. This R21 application embodies a high-risk, high-reward approach to obesity research. It ventures into uncharted territory by proposing that mEVs are novel regulators of metabolic programming, a concept that has not been explored in prior studies. The potential reward is substantial: discovering a new mechanism by which maternal obesity influences offspring health could fundamentally shift our understanding of early-life metabolic programming and lead to innovative strategies for obesity prevention. If successful, this research could open a new field of study with broad implications for maternal and child health.

Avian influenza virus prevention in the domestic host by a deactivated vaccine

Abstract Influenza viruses, which affect both birds and mammals, pose a substantial public health concern. An estimated 10% of the global population annually becomes infected, resulting in 300,000 to 600,000 deaths worldwide. Our research objectives are to develop a Hemagglutinin (HA) and Neuraminidase (NA) based rabies-vectored vaccine against highly pathogenic Avian Influenza (HPAI) A virus H5N1. We have already demonstrated the vaccine’s immunogenicity and protective efficacy against HPAI H5N1 Vietnam 1203. To advance this research, we propose to utilize a novel RAVB-based deactivated vaccine that harbors the H5 antigens of the current homologous circulation (clade 2.3.4.4b) and a construct expressing N1. Our first aim will involve comparing the H5 or H5/N1 RABV-based vaccines against challenges by PR8 recombinants carrying H5N1 proteins in mice. We will employ a single immunization and a prime/boost approach, either with or without an adjuvant approved for use in animals and humans (SEPIVAC SWE™). We will assess the role of T cells in the vaccine-induced protection by performing CD4/CD8 depletion before challenge Our second aim will utilize the vaccine approach identified to protect our mouse system in dairy cows. Subsequently, we will assess the vaccine’s efficacy against challenges administered intranasally and intramammary. We will verify the role of the vaccine-induced antibodies in protection against H5N1 by performing passive transfer studies of purified IgG from vaccinated cows before challenge. In summary, this study will evaluate the efficacy and delineate the mechanism of protection of a safe and well- established vaccine platform to protect against HPAI H5 and explore its potential as an animal and human vaccine.

Targeting subtype specification as a driver of PDAC health disparities

PROJECT SUMMARY Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease that is refractory to current treatment strategies due in part to adaptive mechanisms of chemoresistance. Racial health disparities also confound the treatment and care of these patients. Blacks (people with African genetic ancestry) have significantly higher incidence rates of PDAC and decreased survival times compared to Caucasians (White genetic ancestry) even after socioeconomic status and tumor stages are controlled. Therefore, it is possible different racial groups exhibit unique molecular characteristics in PDAC tumors that contribute to these health disparities. The unique molecular characteristics that distinguish PDAC tumors between racial groups exhibiting disparities have the potential to identify new therapeutic targets. In a previous study, we identified 4 distinct subtypes of PDAC (Metabolic, Progenitor-like, Proliferative, and Inflammatory) that can be distinguished using multivariate analysis of quantitative proteomic data. While these PDAC subtypes are predictive of therapeutic response, this has not yet been analyzed in disparity factor balanced studies. We have examined the proteomes of primary PDAC tumors using quantitative mass spectrometry and identified unique protein signatures for Blacks and Whites. PDAC tumors from Black patients display features consistent with the Inflammatory subtype of PDAC, which is characterized by an inflamed microenvironment expressing complement proteins that can promote resistance to chemotherapy. Therefore, it is possible that race influences subtype and Blacks could preferentially develop the more aggressive and treatment refractory Inflammatory subtype. Strategies are needed to modulate subtype to improve response to chemotherapy. Toward this goal, our proteomic analysis identified polycomb repressor complex 1 (PRC1) protein RNF2 as being upregulated in PDACs from Blacks compared to Whites. We have also discovered that RNF2 regulates mRNA expression of the PDAC subtype specification factor GATA6 and inhibiting RNF2 promotes a molecular shift toward the more chemosensitive Classical subtype of PDAC. Therapeutic targeting can be achieved with Tazemetostat that inhibits the upstream PRC2 to prevent RNF2 binding the GATA6 promoter leading to its increased expression. Additionally, the Inflammatory subtype characterized by innate immune complement protein activation could be targeted with another FDA approved drug, Avacopan, which has not previously been studied in PDAC. Therefore, the Specific Aims of this proposal are designed to: 1) Evaluate the extent to which Tazemetostat treatment impacts chemotherapy-induced subtype plasticity in patient derived organoids; and 2) To determine the extent to which strategies targeting pathways associated with PDAC disparities affect progression and subtype characteristics in vivo. The successful completion of these aims has the potential to be moved quickly into phase I clinical trials since both Tazemetostat and Avacopan are FDA approved drugs. Furthermore, if successful, this project has the potential to mitigate health disparities in PDAC and broadly improve patient outcomes by implementing new precision interventions. The mouse models we propose faithfully recapitulate pancreatic cancer's clinical syndrome, histopathology and molecular properties, including the often-unique features of the stromal and immune responses that constitute the complex desmoplasia of this disease, which cannot be addressed using in vitro model systems

Development of a multi-modal mouse model of cluster headache

PROJECT SUMMARY / ABSTRACT Cluster headache (CH), which affects about 1 in 1,000 people, is a severe and debilitating primary headache disorder characterized by repeated attacks occurring in clusters over weeks or months. CH has clearly defined features: severe pain (worse than childbirth), facial autonomic changes (such as a watery eye), restlessness, and a striking circadian pattern of attacks (at the same time each day like clockwork in approximately 70.5% of patients). CH also has a well-defined pathophysiology of 3 systems: the trigeminovascular pain system, the autonomic nervous system, and the hypothalamic system (in particular the posterior hypothalamus, the first brain area activated during an attack). Despite the well-known features and systems involved in CH, no disease- specific treatments are available: all CH treatments are repurposed medications from other diseases. This lack of CH-specific treatments is due in large part to the lack of a viable animal model that faithfully recapitulates the aforementioned CH features. To develop a specific animal model for CH, we previously studied a trigeminovascular headache model (repeated nitroglycerin injections), and discovered a circadian pattern of pain responses that reflects the clockwork-like pattern of attacks in CH patients. Furthermore, our analysis also identified a recently discovered CH modifier gene Mertk (MER proto-oncogene, tyrosine receptor kinase) to be highly rhythmically expressed in the trigeminal ganglion. Deletion of Mertk (Mertk-KO) altered the normal circadian rhythm of pain sensitivity by increasing pain sensitivity over 24 hours. Finally, activation of the posterior hypothalamus (via c-Fos staining) was observed after NTG administration in wild-type mice. Based on these exciting preliminary findings, we hypothesize that a combination of trigeminovascular (nitroglycerin), genetic (Mertk-KO), and hypothalamic (direct optogenetic activation of the posterior hypothalamus) manipulations will generate the first multi-modal animal model of CH. In Aim 1 (the R61 phase), we will determine the contributions of each aspect of our combined model, alone or in combination (a 4x2 grid of NTG or control, Mertk KO mouse or wild-type control, and optogenetic injection or control). Our milestone for progression to the R33 phase will be significant differences in at least two pain behaviors in our model compared to controls. In Aims 2 and 3 (the R33 phase), we will validate our model through face validity (lacrimation and restlessness), construct validity (CGRP, PACAP, and VIP in the trigeminal ganglion and hypothalamus), and predictive validity (ability of first-line and new treatments to ameliorate the pain behaviors of our model). This project is highly significant and innovative, addressing a profound need for a specific and comprehensive animal model for this devastating yet understudied disease. With the unique combination of complementary expertise in CH (laboratory and clinical), circadian biology, pharmacology, optogenetics and pain, we are ideally suited to generate this combined CH model with the goal of providing insights into CH pathophysiology and developing novel therapeutics.

MRI investigation of orientation-dependent changes in microstructure and function in a mouse model of mild traumatic brain injury

Spike train structure of cortical transcriptomic populations in vivo

The cortex comprises many neuronal types, which can be distinguished by their transcriptomes: the sets of genes they express. Little is known about the in vivo activity of these cell types, particularly as regards the structure of their spike trains, which might provide clues to cortical circuit function. To address this question, we used Neuropixels electrodes to record layer 5 excitatory populations in mouse V1, then transcriptomically identified the recorded cell types. To do so, we performed a subsequent recording of the same cells using 2-photon (2p) calcium imaging, identifying neurons between the two recording modalities by fingerprinting their responses to a “zebra noise” stimulus and estimating the path of the electrode through the 2p stack with a probabilistic method. We then cut brain slices and performed in situ transcriptomics to localize ~300 genes using coppaFISH3d, a new open source method, and aligned the transcriptomic data to the 2p stack. Analysis of the data is ongoing, and suggests substantial differences in spike time coordination between ET and IT neurons, as well as between transcriptomic subtypes of both these excitatory types.

Memory Decoding Journal Club: Functional connectomics reveals general wiring rule in mouse visual cortex

Functional connectomics reveals general wiring rule in mouse visual cortex

Astrocytes: From Metabolism to Cognition

Different brain cell types exhibit distinct metabolic signatures that link energy economy to cellular function. Astrocytes and neurons, for instance, diverge dramatically in their reliance on glycolysis versus oxidative phosphorylation, underscoring that metabolic fuel efficiency is not uniform across cell types. A key factor shaping this divergence is the structural organization of the mitochondrial respiratory chain into supercomplexes. Specifically, complexes I (CI) and III (CIII) form a CI–CIII supercomplex, but the degree of this assembly varies by cell type. In neurons, CI is predominantly integrated into supercomplexes, resulting in highly efficient mitochondrial respiration and minimal reactive oxygen species (ROS) generation. Conversely, in astrocytes, a larger fraction of CI remains unassembled, freely existing apart from CIII, leading to reduced respiratory efficiency and elevated mitochondrial ROS production. Despite this apparent inefficiency, astrocytes boast a highly adaptable metabolism capable of responding to diverse stressors. Their looser CI–CIII organization allows for flexible ROS signaling, which activates antioxidant programs via transcription factors like Nrf2. This modular architecture enables astrocytes not only to balance energy production but also to support neuronal health and influence complex organismal behaviors.

Neural mechanisms of optimal performance

When we attend a demanding task, our performance is poor at low arousal (when drowsy) or high arousal (when anxious), but we achieve optimal performance at intermediate arousal. This celebrated Yerkes-Dodson inverted-U law relating performance and arousal is colloquially referred to as being "in the zone." In this talk, I will elucidate the behavioral and neural mechanisms linking arousal and performance under the Yerkes-Dodson law in a mouse model. During decision-making tasks, mice express an array of discrete strategies, whereby the optimal strategy occurs at intermediate arousal, measured by pupil, consistent with the inverted-U law. Population recordings from the auditory cortex (A1) further revealed that sound encoding is optimal at intermediate arousal. To explain the computational principle underlying this inverted-U law, we modeled the A1 circuit as a spiking network with excitatory/inhibitory clusters, based on the observed functional clusters in A1. Arousal induced a transition from a multi-attractor (low arousal) to a single attractor phase (high arousal), and performance is optimized at the transition point. The model also predicts stimulus- and arousal-induced modulations of neural variability, which we confirmed in the data. Our theory suggests that a single unifying dynamical principle, phase transitions in metastable dynamics, underlies both the inverted-U law of optimal performance and state-dependent modulations of neural variability.

Memory Decoding Journal Club: "Synaptic architecture of a memory engram in the mouse hippocampus

Synaptic architecture of a memory engram in the mouse hippocampus

Retinal input integration in excitatory and inhibitory neurons in the mouse superior colliculus in vivo

Analyzing Network-Level Brain Processing and Plasticity Using Molecular Neuroimaging

Behavior and cognition depend on the integrated action of neural structures and populations distributed throughout the brain. We recently developed a set of molecular imaging tools that enable multiregional processing and plasticity in neural networks to be studied at a brain-wide scale in rodents and nonhuman primates. Here we will describe how a novel genetically encoded activity reporter enables information flow in virally labeled neural circuitry to be monitored by fMRI. Using the reporter to perform functional imaging of synaptically defined neural populations in the rat somatosensory system, we show how activity is transformed within brain regions to yield characteristics specific to distinct output projections. We also show how this approach enables regional activity to be modeled in terms of inputs, in a paradigm that we are extending to address circuit-level origins of functional specialization in marmoset brains. In the second part of the talk, we will discuss how another genetic tool for MRI enables systematic studies of the relationship between anatomical and functional connectivity in the mouse brain. We show that variations in physical and functional connectivity can be dissociated both across individual subjects and over experience. We also use the tool to examine brain-wide relationships between plasticity and activity during an opioid treatment. This work demonstrates the possibility of studying diverse brain-wide processing phenomena using molecular neuroimaging.

Mouse Motor Cortex Circuits and Roles in Oromanual Behavior

I’m interested in structure-function relationships in neural circuits and behavior, with a focus on motor and somatosensory areas of the mouse’s cortex involved in controlling forelimb movements. In one line of investigation, we take a bottom-up, cellularly oriented approach and use optogenetics, electrophysiology, and related slice-based methods to dissect cell-type-specific circuits of corticospinal and other neurons in forelimb motor cortex. In another, we take a top-down ethologically oriented approach and analyze the kinematics and cortical correlates of “oromanual” dexterity as mice handle food. I'll discuss recent progress on both fronts.

Understanding the complex behaviors of the ‘simple’ cerebellar circuit

Every movement we make requires us to precisely coordinate muscle activity across our body in space and time. In this talk I will describe our efforts to understand how the brain generates flexible, coordinated movement. We have taken a behavior-centric approach to this problem, starting with the development of quantitative frameworks for mouse locomotion (LocoMouse; Machado et al., eLife 2015, 2020) and locomotor learning, in which mice adapt their locomotor symmetry in response to environmental perturbations (Darmohray et al., Neuron 2019). Combined with genetic circuit dissection, these studies reveal specific, cerebellum-dependent features of these complex, whole-body behaviors. This provides a key entry point for understanding how neural computations within the highly stereotyped cerebellar circuit support the precise coordination of muscle activity in space and time. Finally, I will present recent unpublished data that provide surprising insights into how cerebellar circuits flexibly coordinate whole-body movements in dynamic environments.

Influence of the context of administration in the antidepressant-like effects of the psychedelic 5-MeO-DMT

Psychedelics like psilocybin have shown rapid and long-lasting efficacy on depressive and anxiety symptoms. Other psychedelics with shorter half-lives, such as DMT and 5-MeO-DMT, have also shown promising preliminary outcomes in major depression, making them interesting candidates for clinical practice. Despite several promising clinical studies, the influence of the context on therapeutic responses or adverse effects remains poorly documented. To address this, we conducted preclinical studies evaluating the psychopharmacological profile of 5-MeO-DMT in contexts previously validated in mice as either pleasant (positive setting) or aversive (negative setting). Healthy C57BL/6J male mice received a single intraperitoneal (i.p.) injection of 5-MeO-DMT at doses of 0.5, 5, and 10 mg/kg, with assessments at 2 hours, 24 hours, and one week post-administration. In a corticosterone (CORT) mouse model of depression, 5-MeO-DMT was administered in different settings, and behavioral tests mimicking core symptoms of depression and anxiety were conducted. In CORT-exposed mice, an acute dose of 0.5 mg/kg administered in a neutral setting produced antidepressant-like effects at 24 hours, as observed by reduced immobility time in the Tail Suspension Test (TST). In a positive setting, the drug also reduced latency to first immobility and total immobility time in the TST. However, these beneficial effects were negated in a negative setting, where 5-MeO-DMT failed to produce antidepressant-like effects and instead elicited an anxiogenic response in the Elevated Plus Maze (EPM).Our results indicate a strong influence of setting on the psychopharmacological profile of 5-MeO-DMT. Future experiments will examine cortical markers of pre- and post-synaptic density to correlate neuroplasticity changes with the behavioral effects of 5-MeO-DMT in different settings.

Investigating dynamiCa++l mechanisms underlying cortical development and disease

Modeling human brain development and disease: the role of primary cilia

Neurodevelopmental disorders (NDDs) impose a global burden, affecting an increasing number of individuals. While some causative genes have been identified, understanding the human-specific mechanisms involved in these disorders remains limited. Traditional gene-driven approaches for modeling brain diseases have failed to capture the diverse and convergent mechanisms at play. Centrosomes and cilia act as intermediaries between environmental and intrinsic signals, regulating cellular behavior. Mutations or dosage variations disrupting their function have been linked to brain formation deficits, highlighting their importance, yet their precise contributions remain largely unknown. Hence, we aim to investigate whether the centrosome/cilia axis is crucial for brain development and serves as a hub for human-specific mechanisms disrupted in NDDs. Towards this direction, we first demonstrated species-specific and cell-type-specific differences in the cilia-genes expression during mouse and human corticogenesis. Then, to dissect their role, we provoked their ectopic overexpression or silencing in the developing mouse cortex or in human brain organoids. Our findings suggest that cilia genes manipulation alters both the numbers and the position of NPCs and neurons in the developing cortex. Interestingly, primary cilium morphology is disrupted, as we find changes in their length, orientation and number that lead to disruption of the apical belt and altered delamination profiles during development. Our results give insight into the role of primary cilia in human cortical development and address fundamental questions regarding the diversity and convergence of gene function in development and disease manifestation. It has the potential to uncover novel pharmacological targets, facilitate personalized medicine, and improve the lives of individuals affected by NDDs through targeted cilia-based therapies.

Cell-type-specific plasticity shapes neocortical dynamics for motor learning

How do cortical circuits acquire new dynamics that drive learned movements? This webinar will focus on mouse premotor cortex in relation to learned lick-timing and explore high-density electrophysiology using our silicon neural probes alongside region and cell-type-specific acute genetic manipulations of proteins required for synaptic plasticity.

Mitochondrial diversity in the mouse and human brain

The basis of the mind, of mental states, and complex behaviors is the flow of energy through microscopic and macroscopic brain structures. Energy flow through brain circuits is powered by thousands of mitochondria populating the inside of every neuron, glial, and other nucleated cell across the brain-body unit. This seminar will cover emerging approaches to study the mind-mitochondria connection and present early attempts to map the distribution and diversity of mitochondria across brain tissue. In rodents, I will present convergent multimodal evidence anchored in enzyme activities, gene expression, and animal behavior that distinct behaviorally-relevant mitochondrial phenotypes exist across large-scale mouse brain networks. Extending these findings to the human brain, I will present a developing systematic biochemical and molecular map of mitochondrial variation across cortical and subcortical brain structures, representing a foundation to understand the origin of complex energy patterns that give rise to the human mind.

Investigating activity-dependent processes during cortical neuronal assembly in development and disease

Cellular and genetic mechanisms of cerebral cortex folding

One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding, both of which emerge during development. Over the last few years, work from my lab has shown that specific cellular and genetic mechanisms play central roles in cortex folding, particularly linked to neural stem and progenitor cells. Key mechanisms include high rates of neurogenesis, high abundance of basal Radial Glia Cells (bRGCs), and neuron migration, all of which are intertwined during development. We have also shown that primary cortical folds follow highly stereotyped patterns, defined by a spatial-temporal protomap of gene expression within germinal layers of the developing cortex. I will present recent findings from my laboratory revealing novel cellular and genetic mechanisms that regulate cortex expansion and folding. We have uncovered the contribution of epigenetic regulation to the establishment of the cortex folding protomap, modulating the expression levels of key transcription factors that control progenitor cell proliferation and cortex folding. At the single cell level, we have identified an unprecedented diversity of cortical progenitor cell classes in the ferret and human embryonic cortex. These are differentially enriched in gyrus versus sulcus regions and establish parallel cell lineages, not observed in mouse. Our findings show that genetic and epigenetic mechanisms in gyrencephalic species diversify cortical progenitor cell types and implement parallel cell linages, driving the expansion of neurogenesis and patterning cerebral cortex folds.

Astrocyte reprogramming / activation and brain homeostasis

Astrocytes are multifunctional glial cells, implicated in neurogenesis and synaptogenesis, supporting and fine-tuning neuronal activity and maintaining brain homeostasis by controlling blood-brain barrier permeability. During the last years a number of studies have shown that astrocytes can also be converted into neurons if they force-express neurogenic transcription factors or miRNAs. Direct astrocytic reprogramming to induced-neurons (iNs) is a powerful approach for manipulating cell fate, as it takes advantage of the intrinsic neural stem cell (NSC) potential of brain resident reactive astrocytes. To this end, astrocytic cell fate conversion to iNs has been well-established in vitro and in vivo using combinations of transcription factors (TFs) or chemical cocktails. Challenging the expression of lineage-specific TFs is accompanied by changes in the expression of miRNAs, that post-transcriptionally modulate high numbers of neurogenesis-promoting factors and have therefore been introduced, supplementary or alternatively to TFs, to instruct direct neuronal reprogramming. The neurogenic miRNA miR-124 has been employed in direct reprogramming protocols supplementary to neurogenic TFs and other miRNAs to enhance direct neurogenic conversion by suppressing multiple non-neuronal targets. In our group we aimed to investigate whether miR-124 is sufficient to drive direct reprogramming of astrocytes to induced-neurons (iNs) on its own both in vitro and in vivo and elucidate its independent mechanism of reprogramming action. Our in vitro data indicate that miR-124 is a potent driver of the reprogramming switch of astrocytes towards an immature neuronal fate. Elucidation of the molecular pathways being triggered by miR-124 by RNA-seq analysis revealed that miR-124 is sufficient to instruct reprogramming of cortical astrocytes to immature induced-neurons (iNs) in vitro by down-regulating genes with important regulatory roles in astrocytic function. Among these, the RNA binding protein Zfp36l1, implicated in ARE-mediated mRNA decay, was found to be a direct target of miR-124, that be its turn targets neuronal-specific proteins participating in cortical development, which get de-repressed in miR-124-iNs. Furthermore, miR-124 is potent to guide direct neuronal reprogramming of reactive astrocytes to iNs of cortical identity following cortical trauma, a novel finding confirming its robust reprogramming action within the cortical microenvironment under neuroinflammatory conditions. In parallel to their reprogramming properties, astrocytes also participate in the maintenance of blood-brain barrier integrity, which ensures the physiological functioning of the central nervous system and gets affected contributing to the pathology of several neurodegenerative diseases. To study in real time the dynamic physical interactions of astrocytes with brain vasculature under homeostatic and pathological conditions, we performed 2-photon brain intravital imaging in a mouse model of systemic neuroinflammation, known to trigger astrogliosis and microgliosis and to evoke changes in astrocytic contact with brain vasculature. Our in vivo findings indicate that following neuroinflammation the endfeet of activated perivascular astrocytes lose their close proximity and physiological cross-talk with vasculature, however this event is at compensated by the cross-talk of astrocytes with activated microglia, safeguarding blood vessel coverage and maintenance of blood-brain integrity.

Bio-realistic multiscale modeling of cortical circuits

A central question in neuroscience is how the structure of brain circuits determines their activity and function. To explore this systematically, we developed a 230,000-neuron model of mouse primary visual cortex (area V1). The model integrates a broad array of experimental data:Distribution and morpho-electric properties of different neuron types in V1.

Circadian modulation by time-restricted feeding rescues brain pathology and improves memory in mouse models of Alzheimer’s disease

Effect of nutrient sensing by microglia on mouse behavior

Microglia are the brain macrophages, eliciting multifaceted functions to maintain brain homeostasis across lifetime. To achieve this, microglia are able to sense a plethora of signals in their close environment. In the lab, we investigate the effect of nutrients on microglia function for several reasons: 1) Microglia express all the cellular machinery required to sense nutrients; 2) Eating habits have changed considerably over the last century, towards diets rich in fats and sugars; 3) This so-called "Western diet" is accompanied by an increase in the occurrence of neuropathologies, in which microglia are known to play a role. In my talk, I will present data showing how variations in nutrient intake alter microglia function, including exacerbation of synaptic pruning, with profound consequences for neuronal activity and behavior. I will also show unpublished data on the mechanisms underlying the effects of nutrients on microglia, notably through the regulation of their metabolic activity.

X-linked mosaicism and behavioral heterogeneity in Rett syndrome

The melanopsin mosaic: exploring the diversity of non-image forming retinal ganglion cells

In this talk, I will focus on recent work that has uncovered the diversity of intrinsically photosensitive retinal ganglion cells (ipRGCs). These are a unique type of retinal ganglion cell that contains the photopigment melanopsin. ipRGCs are the retinal neurons responsible for driving non-imaging forming behaviors and reflexes, such as circadian entrainment and pupil constriction, amongst many others. My lab has recently focused on uncovering the diversity of ipRGCs, their distribution throughout the mammalian retina, and their axon projections in the brain.

Spatial and Single Cell Genomics for Next Generation Neuroscience

The advent of next generation sequencing ushered in a ten-year period of exuberant technology development, enabling the quantification of gene expression and epigenetic features within individual cells, and within intact tissue sections.  In this seminar, I will outline our technological contributions, beginning with the development of Drop-seq, a method for high-throughput single cell analysis, followed by the development of Slide-seq, a technique for measuring genome-wide expression at 10 micron spatial resolution.  Using a combination of these techniques, we recently constructed a comprehensive cell type atlas of the adult mouse brain, positioning cell types within individual brain structures.  I will discuss the major findings from this dataset, including emerging principles of neurotransmission, and the localization of disease gene signatures to specific cell types.  Finally, I will introduce a new spatial technology, Slide-tags, that unifies single cell and spatial genomics into a single, highly scalable assay.

Cellular crosstalk in Neurodevelopmental Disorders

Cellular crosstalk is an essential process during brain development and it is influenced by numerous factors, including the morphology of the cells, their adhesion molecules, the local extracellular matrix and the secreted vesicles. Inspired by mutations associated with neurodevelopmental disorders, we focus on understanding the role of extracellular mechanisms essential for the correct development of the human brain. Hence, we combine the in vivo mouse model and the in vitro human-derived neurons, cerebral organoids, and dorso-ventral assembloids in order to better comprehend the molecular and cellular mechanisms involved in ventral progenitors’ proliferation and fate as well as migration and maturation of inhibitory neurons during human brain development and tackle the causes of neurodevelopmental disorders. We particularly focus on mutations in genes influencing cell-cell contacts, extracellular matrix, and secretion of vesicles and therefore study intrinsic and extrinsic mechanisms contributing to the formation of the brain. Our data reveal an important contribution of cell non-autonomous mechanisms in the development of neurodevelopmental disorders.

Comparative transcriptomics of retinal cell types

In vivo direct imaging of neuronal activity at high temporospatial resolution

Advanced noninvasive neuroimaging methods provide valuable information on the brain function, but they have obvious pros and cons in terms of temporal and spatial resolution. Functional magnetic resonance imaging (fMRI) using blood-oxygenation-level-dependent (BOLD) effect provides good spatial resolution in the order of millimeters, but has a poor temporal resolution in the order of seconds due to slow hemodynamic responses to neuronal activation, providing indirect information on neuronal activity. In contrast, electroencephalography (EEG) and magnetoencephalography (MEG) provide excellent temporal resolution in the millisecond range, but spatial information is limited to centimeter scales. Therefore, there has been a longstanding demand for noninvasive brain imaging methods capable of detecting neuronal activity at both high temporal and spatial resolution. In this talk, I will introduce a novel approach that enables Direct Imaging of Neuronal Activity (DIANA) using MRI that can dynamically image neuronal spiking activity in milliseconds precision, achieved by data acquisition scheme of rapid 2D line scan synchronized with periodically applied functional stimuli. DIANA was demonstrated through in vivo mouse brain imaging on a 9.4T animal scanner during electrical whisker-pad stimulation. DIANA with milliseconds temporal resolution had high correlations with neuronal spike activities, which could also be applied in capturing the sequential propagation of neuronal activity along the thalamocortical pathway of brain networks. In terms of the contrast mechanism, DIANA was almost unaffected by hemodynamic responses, but was subject to changes in membrane potential-associated tissue relaxation times such as T2 relaxation time. DIANA is expected to break new ground in brain science by providing an in-depth understanding of the hierarchical functional organization of the brain, including the spatiotemporal dynamics of neural networks.

Light-driven dopamine release in the adult and developing retina

NOTE: DUE TO A CYBER ATTACK OUR UNIVERSITY WEB SYSTEM IS SHUT DOWN - TALK WILL BE RESCHEDULED

The size and structure of the dendritic arbor play important roles in determining how synaptic inputs of neurons are converted to action potential output and how neurons are integrated in the surrounding neuronal network. Accordingly, neurons with aberrant morphology have been associated with neurological disorders. Dysmorphic, enlarged neurons are, for example, a hallmark of focal epileptogenic lesions like focal cortical dysplasia (FCDIIb) and gangliogliomas (GG). However, the regulatory mechanisms governing the development of dendrites are insufficiently understood. The evolutionary conserved Ste20/Hippo kinase pathway has been proposed to play an important role in regulating the formation and maintenance of dendritic architecture. A key element of this pathway, Ste20-like kinase (SLK), regulates cytoskeletal dynamics in non-neuronal cells and is strongly expressed throughout neuronal development. Nevertheless, its function in neurons is unknown. We found that during development of mouse cortical neurons, SLK has a surprisingly specific role for proper elaboration of higher, ≥ 3rd, order dendrites both in cultured neurons and living mice. Moreover, SLK is required to maintain excitation-inhibition balance. Specifically, SLK knockdown causes a selective loss of inhibitory synapses and functional inhibition after postnatal day 15, while excitatory neurotransmission is unaffected. This mechanism may be relevant for human disease, as dysmorphic neurons within human cortical malformations exhibit significant loss of SLK expression. To uncover the signaling cascades underlying the action of SLK, we combined phosphoproteomics, protein interaction screens and single cell RNA seq. Overall, our data identifies SLK as a key regulator of both dendritic complexity during development and of inhibitory synapse maintenance.

Neural circuits for vision in the natural world

Circuit mechanisms of attention dysfunction in Scn8a+/- mice: implications for epilepsy and neurodevelopmental disorders

Perivascular cells induce microglial phagocytic states and synaptic engulfment via SPP1 in mouse models of Alzheimer's disease

Epigenetic rewiring in Schinzel-Giedion syndrome

During life, a variety of specialized cells arise to grant the right and timely corrected functions of tissues and organs. Regulation of chromatin in defining specialized genomic regions (e.g. enhancers) plays a key role in developmental transitions from progenitors into cell lineages. These enhancers, properly topologically positioned in 3D space, ultimately guide the transcriptional programs. It is becoming clear that several pathologies converge in differential enhancer usage with respect to physiological situations. However, why some regulatory regions are physiologically preferred, while some others can emerge in certain conditions, including other fate decisions or diseases, remains obscure. Schinzel-Giedion syndrome (SGS) is a rare disease with symptoms such as severe developmental delay, congenital malformations, progressive brain atrophy, intractable seizures, and infantile death. SGS is caused by mutations in the SETBP1 gene that results in its accumulation further leading to the downstream accumulation of SET. The oncoprotein SET has been found as part of the histone chaperone complex INHAT that blocks the activity of histone acetyltransferases suggesting that SGS may (i) represent a natural model of alternative chromatin regulation and (ii) offer chances to study downstream (mal)adaptive mechanisms. I will present our work on the characterization of SGS in appropriate experimental models including iPSC-derived cultures and mouse.

The strongly recurrent regime of cortical networks

Modern electrophysiological recordings simultaneously capture single-unit spiking activities of hundreds of neurons. These neurons exhibit highly complex coordination patterns. Where does this complexity stem from? One candidate is the ubiquitous heterogeneity in connectivity of local neural circuits. Studying neural network dynamics in the linearized regime and using tools from statistical field theory of disordered systems, we derive relations between structure and dynamics that are readily applicable to subsampled recordings of neural circuits: Measuring the statistics of pairwise covariances allows us to infer statistical properties of the underlying connectivity. Applying our results to spontaneous activity of macaque motor cortex, we find that the underlying network operates in a strongly recurrent regime. In this regime, network connectivity is highly heterogeneous, as quantified by a large radius of bulk connectivity eigenvalues. Being close to the point of linear instability, this dynamical regime predicts a rich correlation structure, a large dynamical repertoire, long-range interaction patterns, relatively low dimensionality and a sensitive control of neuronal coordination. These predictions are verified in analyses of spontaneous activity of macaque motor cortex and mouse visual cortex. Finally, we show that even microscopic features of connectivity, such as connection motifs, systematically scale up to determine the global organization of activity in neural circuits.

Visual circuits for threat anticipation

A specialized role for entorhinal attractor dynamics in combining path integration and landmarks during navigation

During navigation, animals estimate their position using path integration and landmarks. In a series of two studies, we used virtual reality and electrophysiology to dissect how these inputs combine to generate the brain’s spatial representations. In the first study (Campbell et al., 2018), we focused on the medial entorhinal cortex (MEC) and its set of navigationally-relevant cell types, including grid cells, border cells, and speed cells. We discovered that attractor dynamics could explain an array of initially puzzling MEC responses to virtual reality manipulations. This theoretical framework successfully predicted both MEC grid cell responses to additional virtual reality manipulations, as well as mouse behavior in a virtual path integration task. In the second study (Campbell*, Attinger* et al., 2021), we asked whether these principles generalize to other navigationally-relevant brain regions. We used Neuropixels probes to record thousands of neurons from MEC, primary visual cortex (V1), and retrosplenial cortex (RSC). In contrast to the prevailing view that “everything is everywhere all at once,” we identified a unique population of MEC neurons, overlapping with grid cells, that became active with striking spatial periodicity while head-fixed mice ran on a treadmill in darkness. These neurons exhibited unique cue-integration properties compared to other MEC, V1, or RSC neurons: they remapped more readily in response to conflicts between path integration and landmarks; they coded position prospectively as opposed to retrospectively; they upweighted path integration relative to landmarks in conditions of low visual contrast; and as a population, they exhibited a lower-dimensional activity structure. Based on these results, our current view is that MEC attractor dynamics play a privileged role in resolving conflicts between path integration and landmarks during navigation. Future work should include carefully designed causal manipulations to rigorously test this idea, and expand the theoretical framework to incorporate notions of uncertainty and optimality.

PIEZO2 in somatosensory neurons coordinates gastrointestinal transit

The transit of food through the gastrointestinal tract is critical for nutrient absorption and survival, and the gastrointestinal tract has the ability to initiate motility reflexes triggered by luminal distention. This complex function depends on the crosstalk between extrinsic and intrinsic neuronal innervation within the intestine, as well as local specialized enteroendocrine cells. However, the molecular mechanisms and the subset of sensory neurons underlying the initiation and regulation of intestinal motility remain largely unknown. Here, we show that humans lacking PIEZO2 exhibit impaired bowel sensation and motility. Piezo2 in mouse dorsal root but not nodose ganglia is required to sense gut content, and this activity slows down food transit rates in the stomach, small intestine, and colon. Indeed, Piezo2 is directly required to detect colon distension in vivo. Our study unveils the mechanosensory mechanisms that regulate the transit of luminal contents throughout the gut, which is a critical process to ensure proper digestion, nutrient absorption, and waste removal. These findings set the foundation of future work to identify the highly regulated interactions between sensory neurons, enteric neurons and non- neuronal cells that control gastrointestinal motility.

Interplay between circuits that mediate spontaneous retinal waves and early light responses during retinal development

Brain mosaicism in epileptogenic cortical malformations

Focal Cortical Dysplasia (FCD) is the most common focal cortical malformation leading to intractable childhood focal epilepsy. In recent years, we and others have shown that FCD type II is caused by mosaic mutations in genes within the PI3K-AKT-mTOR-signaling pathway. Hyperactivation of the mTOR pathway accounts for neuropathological abnormalities and seizure occurrence in FCD. We further showed from human surgical FCDII tissue that epileptiform activity correlates with the density of mutated dysmorphic neurons, supporting their pro-epileptogenic role. The level of mosaicism, as defined by variant allele frequency (VAF) is thought to correlate with the size and regional brain distribution of the lesion such that when a somatic mutation occurs early during the cortical development, the dysplastic area is smaller than if it occurs later. Novel approaches based on the detection of cell-free DNA from the CSF and from trace tissue adherent to SEEG electrodes promise future opportunities for genetic testing during the presurgical evaluation of refractory epilepsy patients or in those that are not eligible for surgery. In utero-based electroporation mouse models allow to express somatic mutation during neurodevelopment and recapitulate most neuropathological and clinical features of FCDII, establishing relevant preclinical mouse models for developing precision medicine strategies.

Programmed axon death: from animal models into human disease

Programmed axon death is a widespread and completely preventable mechanism in injury and disease. Mouse and Drosophila studies define a molecular pathway involving activation of SARM1 NA Dase and its prevention by NAD synthesising enzyme NMNAT2 . Loss of axonal NMNAT2 causes its substrate, NMN , to accumulate and activate SARM1 , driving loss of NAD and changes in ATP , ROS and calcium. Animal models caused by genetic mutation, toxins, viruses or metabolic defects can be alleviated by blocking programmed axon death, for example models of CMT1B , chemotherapy-induced peripheral neuropathy (CIPN), rabies and diabetic peripheral neuropathy (DPN). The perinatal lethality of NMNAT2 null mice is completely rescued, restoring a normal, healthy lifespan. Animal models lack the genetic and environmental diversity present in human populations and this is problematic for modelling gene-environment combinations, for example in CIPN and DPN , and identifying rare, pathogenic mutations. Instead, by testing human gene variants in WGS datasets for loss- and gain-of-function, we identified enrichment of rare SARM1 gain-of-function variants in sporadic ALS , despite previous negative findings in SOD1 transgenic mice. We have shown in mice that heterozygous SARM1 loss-of-function is protective from a range of axonal stresses and that naturally-occurring SARM1 loss-of-function alleles are present in human populations. This enables new approaches to identify disorders where blocking SARM1 may be therapeutically useful, and the existence of two dominant negative human variants in healthy adults is some of the best evidence available that drugs blocking SARM1 are likely to be safe. Further loss- and gain-of-function variants in SARM1 and NMNAT2 are being identified and used to extend and strengthen the evidence of association with neurological disorders. We aim to identify diseases, and specific patients, in whom SARM1 -blocking drugs are most likely to be effective.

Love, death, and oxytocin: the challenges of mouse maternal care

Dynamics of cortical circuits: underlying mechanisms and computational implications

A signature feature of cortical circuits is the irregularity of neuronal firing, which manifests itself in the high temporal variability of spiking and the broad distribution of rates. Theoretical works have shown that this feature emerges dynamically in network models if coupling between cells is strong, i.e. if the mean number of synapses per neuron K is large and synaptic efficacy is of order 1/\sqrt{K}. However, the degree to which these models capture the mechanisms underlying neuronal firing in cortical circuits is not fully understood. Results have been derived using neuron models with current-based synapses, i.e. neglecting the dependence of synaptic current on the membrane potential, and an understanding of how irregular firing emerges in models with conductance-based synapses is still lacking. Moreover, at odds with the nonlinear responses to multiple stimuli observed in cortex, network models with strongly coupled cells respond linearly to inputs. In this talk, I will discuss the emergence of irregular firing and nonlinear response in networks of leaky integrate-and-fire neurons. First, I will show that, when synapses are conductance-based, irregular firing emerges if synaptic efficacy is of order 1/\log(K) and, unlike in current-based models, persists even under the large heterogeneity of connections which has been reported experimentally. I will then describe an analysis of neural responses as a function of coupling strength and show that, while a linear input-output relation is ubiquitous at strong coupling, nonlinear responses are prominent at moderate coupling. I will conclude by discussing experimental evidence of moderate coupling and loose balance in the mouse cortex.

How do Astrocytes Sculpt Synaptic Circuits?

From symptoms to circuits in Fragile X syndrome

Protective microglial signaling in Alzheimer's Disease

Recent studies have begun to reveal critical roles for the brain’s professional phagocytes, microglia, and their receptors in the control of neurotoxic amyloid beta (Aβ) and myelin debris accumulation in neurodegenerative disease. However, the critical intracellular molecules that orchestrate neuroprotective functions of microglia remain poorly understood. In our studies, we find that targeted deletion of SYK in microglia leads to exacerbated Aβ deposition, aggravated neuropathology, and cognitive defects in the 5xFAD mouse model of Alzheimer’s disease (AD). Disruption of SYK signaling in this AD model was further shown to impede the development of disease-associated microglia (DAM), alter AKT/GSK3β-signaling, and restrict Aβ phagocytosis by microglia. Conversely, receptor-mediated activation of SYK limits Aβ load. We also found that SYK critically regulates microglial phagocytosis and DAM acquisition in demyelinating disease. Collectively, these results broaden our understanding of the key innate immune signaling molecules that instruct beneficial microglial functions in response to neurotoxic material." https://doi.org/10.1016/j.cell.2022.09.030

Convex neural codes in recurrent networks and sensory systems

Neural activity in many sensory systems is organized on low-dimensional manifolds by means of convex receptive fields. Neural codes in these areas are constrained by this organization, as not every neural code is compatible with convex receptive fields. The same codes are also constrained by the structure of the underlying neural network. In my talk I will attempt to provide answers to the following natural questions: (i) How do recurrent circuits generate codes that are compatible with the convexity of receptive fields? (ii) How can we utilize the constraints imposed by the convex receptive field to understand the underlying stimulus space. To answer question (i), we describe the combinatorics of the steady states and fixed points of recurrent networks that satisfy the Dale’s law. It turns out the combinatorics of the fixed points are completely determined by two distinct conditions: (a) the connectivity graph of the network and (b) a spectral condition on the synaptic matrix. We give a characterization of exactly which features of connectivity determine the combinatorics of the fixed points. We also find that a generic recurrent network that satisfies Dale's law outputs convex combinatorial codes. To address question (ii), I will describe methods based on ideas from topology and geometry that take advantage of the convex receptive field properties to infer the dimension of (non-linear) neural representations. I will illustrate the first method by inferring basic features of the neural representations in the mouse olfactory bulb.

Versatile treadmill system for measuring locomotion and neural activity in head-fixed mice

Here, we present a protocol for using a versatile treadmill system to measure locomotion and neural activity at high temporal resolution in head-fixed mice. We first describe the assembly of the treadmill system. We then detail surgical implantation of the headplate on the mouse skull, followed by habituation of mice to locomotion on the treadmill system. The system is compact, movable, and simple to synchronize with other data streams, making it ideal for monitoring brain activity in diverse behavioral frameworks. https://dx.doi.org/10.1016/j.xpro.2022.101701

Dysregulated Translation in Fragile X Syndrome

Hypothalamic episode generators underlying the neural control of fertility

The hypothalamus controls diverse homeostatic functions including fertility. Neural episode generators are required to drive the intermittent pulsatile and surge profiles of reproductive hormone secretion that control gonadal function. Studies in genetic mouse models have been fundamental in defining the neural circuits forming these central pattern generators and the full range of in vitro and in vivo optogenetic and chemogenetic methodologies have enabled investigation into their mechanism of action. The seminar will outline studies defining the hypothalamic “GnRH pulse generator network” and current understanding of its operation to drive pulsatile hormone secretion.

Context-dependent selectivity to natural scenes in the retina

A census of neural timescales across the mouse brain

Bernstein Conference 2024

Exploring the neuroprotective effect of auditory enhanced slow-wave sleep in a mouse model of Alzheimer’s disease

FENS Forum 2024

Spatial scale and coordinates of motion representation in the mouse Nucleus of the Optic Tract

Bernstein Conference 2024

Reconciling Diverse Experimental Findings on Inhibitory Tuning in the Mouse Visual Cortex

Bernstein Conference 2024

Toward a biophysically-detailed, fully-differentiable model of the mouse retina

Bernstein Conference 2024

Distinct aversive states in the mouse medial prefrontal cortex.

COSYNE 2022

Coarse-to-fine processing drives the efficient coding of natural scenes in mouse visual cortex

COSYNE 2022

Label-free biomolecular spectroscopy with vibrational fiber photometry deep in the mouse brain

FENS Forum 2024

Disentangling Fast Representational Drift in Mouse Visual Cortex

COSYNE 2022

The dynamical regime of mouse visual cortex shifts from cooperation to competition with increasing visual input

COSYNE 2022

Emergence of an orientation map in the mouse superior colliculus from stage III retinal waves

COSYNE 2022

Inception loops reveal novel spatially-localized phase invariance in mouse primary visual cortex

COSYNE 2022

Inception loops reveal novel spatially-localized phase invariance in mouse primary visual cortex

COSYNE 2022

Input-specific regulation of locus coeruleus activity for mouse maternal behavior

COSYNE 2022

Input-specific regulation of locus coeruleus activity for mouse maternal behavior

COSYNE 2022

Internally Organized Abstract Task Maps in the Mouse Medial Frontal Cortex

COSYNE 2022

Internally Organized Abstract Task Maps in the Mouse Medial Frontal Cortex

COSYNE 2022

An interpretable spline-LNP model to characterize feedforward and feedback processing in mouse dLGN

COSYNE 2022

An interpretable spline-LNP model to characterize feedforward and feedback processing in mouse dLGN

COSYNE 2022

Isolated correlates of somatosensory perception in the posterior mouse cortex

COSYNE 2022

Isolated correlates of somatosensory perception in the posterior mouse cortex

COSYNE 2022

Predictability in the spiking activity of mouse visual cortex decreases along the processing hierarchy

COSYNE 2022

Predictability in the spiking activity of mouse visual cortex decreases along the processing hierarchy

COSYNE 2022

Predictive coding of global sequence violation in the mouse auditory cortex

COSYNE 2022

Predictive coding of global sequence violation in the mouse auditory cortex

COSYNE 2022

Processing of visual textures in the mouse visual cortex

COSYNE 2022

Processing of visual textures in the mouse visual cortex

COSYNE 2022

Reward modulates visual responses in mouse superior colliculus independently of arousal

COSYNE 2022

Reward modulates visual responses in mouse superior colliculus independently of arousal

COSYNE 2022

Self-assembly of the mammalian neocortex, from mouse to macaque

COSYNE 2022

Self-assembly of the mammalian neocortex, from mouse to macaque

COSYNE 2022

The desire to know: representations of information value in mouse orbitofrontal cortex during information seeking

COSYNE 2023

Circuit-based framework for fine spatial scale clustering of orientation tuning in mouse V1

COSYNE 2023

Directly comparing fly and mouse visual systems reveals algorithmic similarities for motion detection

COSYNE 2023

Distinct brain states modulate visual cortical processing in mouse

COSYNE 2023

Locomotion is associated with straighter neural trajectories for natural movies in mouse visual cortex

COSYNE 2023

Mouse visual cortex as a limited-resource system that self-learns a task-general representation

COSYNE 2023

Myelin loss disrupts neural synchrony directing skilled motor behavior in mouse primary motor cortex

COSYNE 2023

The neural representation of perceptual uncertainty in mouse visual cortex

COSYNE 2023

Analysis of burst sequences in mouse prefrontal cortex during learning

Bernstein Conference 2024